Claims of abrogation of Qur’anic verses ( and which verses are abrogated ) are not accepted by all Muslims. Indeed when they are brought up in the context of jihad, it is generally by extremists. So:
*Bin Ladin’s choice of verses to support his arguments shows that he holds a particular position on a complex question of Quranic interpretation, al-nasikh wa-l-mansukh – the so-called “abrogating and abrogated verses”.[9] The notion originates from the interpretation of a number of Qur’anic verses and from the fact that the Qur’an was not revealed all at once but piece by piece, in such a way that some interpret certain later revelations as replacements for earlier ones. “None of Our revelations do We ‘abrogate’ (nansakh) or cause to be forgotten, but We substitute something better or similar. Do you not know that God has power over all things?” (2:106).[10] “When We substitute (baddalna) one revelation for another – and God knows best what He reveals (in stages) – they say ‘You are nothing but a forger!’ But most of them do not understand” (16:101). “God blots out (yamhu) or confirms what He pleases; with Him is the Mother of the Book” (13:39).
Quotation marks around the word “abrogate” in the above translation of Qur’an 2:106 indicate that the meaning of the word is not uncontested. While Ibn Salamah gives only one possibility: “to abolish” or “remove” (rafa’a)[11], al-Nahhas says that it derives from two things: “to obliterate” (azala) as the sun obliterates the shade, and “to transcribe” (naqala), as when a scribe copies a book.[12] Several types of naskh were identified: one in which the legal principle was changed but not the Qur’anic text itself, another in which the text was changed but not the legal principle, and a third in which both the text and the principle had been removed. Nor did the authorities agree on which were the abrogated and abrogating verses, and how many of them there were: al-Suyuti said 20, al-Nahhas 134, Ibn Salamah 213, and the Shi’ite sources 571![13]
While many continue to believe that the legal implications of certain parts of the Qur’an have been abrogated, some scholars are re-examining the principle of eternality of the Last Revelation and have concluded that “abrogation” refers not to parts of the Qur’an but to previous laws imposed on the Semitic peoples. The laws of Leviticus, Numbers, and Deuteronomy may have been removed by the Qur’an, but in the Qur’an itself there is no abrogation.[14] Furthermore, they maintain, careful reading will demonstrate that abrogation is not needed because there is no conflict in revelations, however widely separated by time and circumstance: when proper cognizance is taken of context, definition, and the grammar of inclusion, exclusion, and exception, apparent contradictions disappear and with them the need for the concept of abrogation.[15] *
From here: http://web.utk.edu/~warda/bin_ladin_and_quran.htm
Some reject the concept of abrogation altogether:
*The abrogation of Quranic verses, arguably the greatest lie against the Quran, was originally invented during the fourth century A.H. (late 10th century A.D.) by some Muslim scholars notably Ahmed Bin Ishaq Al-Dinary (died 318 A.H.), Mohamad Bin Bahr Al-Asbahany (died 322 A.H.), Hebat Allah Bin Salamah (died 410 A.H.) and Mohamad Bin Mousa Al-Hazmy (died 548 A.H.), whose book about Al-Nasekh and Al-Mansoukh is regarded as one of the leading references in the subject. *
from here: http://www.submission.org/abrogation.html
More specifically on Surah 9:5 :
*Surah 9
VERSE 1
**“Freedom from obligation (or ultimatum) is herein issued from GOD and His messenger to the idol worshipers with whom you have entered into a treaty with.” **
VERSE 2
"Therefore, roam the earth freely for four months, and know that you cannot escape from GOD, and that GOD humiliates the disbelievers."
VERSE 3
**“A proclamation is herein issued from GOD and His messenger to all the people on the great day of pilgrimage, that GOD has disowned the idol worshipers, and so did His messenger. Thus, if you repent, it would be better for you. But if you turn away, then know that you can never escape from GOD. Promise those who disbelieve a painful retribution.” **
VERSE 4
**“If the idol worshipers sign a peace treaty with you, and do not violate it, nor band together with others against you, you shall fulfil your treaty with them until the expiration date. GOD loves the righteous.” **
VERSE 5
"Once the Sacred Months are past, (and they refuse to make peace) you may kill the idol worshipers when you encounter them, punish them, and resist every move they make. If they repent and observe the Contact Prayers (Salat) and give the obligatory charity (Zakat), you shall let them go. GOD is Forgiver, Most Merciful."
After reading the five verses together the following matters becomes apparent:
1- Verse 5 speaks of the idol worshippers who are AT WAR with the believers and not any idol worshippers. The words : “the idol worshipers with whom you have entered into a treaty with” in verse 1 confirms that matter since no treaty is entered into unless there is a war situation……
2- In verse 2 God address’s the idol worshippers and tells them that they may roam freely during the four sacred months (since the believers are prohibited from fighting in these months), but that at the end they will not escape from God.
3- In verse 4 it is once again confirmed that the believers are not to attack the idol worshippers who have signed a treaty with them and who do not violate it.
4- Following that, in verse 5 God says that when the sacred months have passed the believers are to fight the idol worshippers.
5- The content of verse 4 (that believers are not to fight idol worshippers who uphold the terms of a treaty) confirms the real meaning of verse 5; the believers are commanded to fight the idol worshippers (outside the sacred months) only at times of war, or when the idol worshippers violate the terms of a treaty (also in a state of war).
This meaning is again confirmed in verse 7 with the words:
“Exempted are those who have signed a peace treaty with you at the Sacred Masjid. If they honour and uphold such a treaty, you shall uphold it as well. GOD loves the righteous.”
In spite of all these indications in the first seven verses of Sura 9 that assert that the fighting may only be directed to the idol worshippers in a state of war, and with those who violate the terms of a peace treaty, yet the abrogation inventors have ignored all the mention of the word ‘treaty’ in these verses and its profound significance. *
From here: http://www.submission.org/4-answering-Islam.htm#author
So, yes, the ObL’s of the world ( along with many early Sunni jurists ) do indeed claim that Sura 9:5 was an abrogating verse. But that is hardly universally accepted in the Muslim world.
A further, rathe skeptical article on abrogation, which does however point out the diversity of opinion on the topic : http://www.rim.org/muslim/clear.htm