I believe you nailed it.
Nice spoiler.
Sort of like the Mad Magazine story where the Secretary of Transportation arranges the death of every other cabinet officer. 
Anybody else note that the last time we saw Jack hiding out from baddies in a warehouse/garage like that (with Audrey I think), it was Tony who showed up to save them in the nick of time. (Season 4, I think).
Tony was plenty willing to kill any number of innocents to do it, though. He seemed perfectly happy to set off the bio-bomb in the subway.
He DID stop the bio-goop rockets, though. Gotta give him kudos for that.
I think it’s more like she had 10 minutes or so before someone came to pick him up and she would lose her shot forever.
Interesting ending. Except for Vampire Jack vs. The Evil Doktors, it was a Jack action-light episode.
-Joe