I wish they would have pulled out Stan's favorite "Get out of Jail Free" card for Doom and said he had diplomatic immunity

t:
IMO they brought Victor in because the stakes were high and they needed all the help they could get since the world would have been destroyed anyway. Like the way the FBI went to Lector in "Silence of the Lambs...because they thought it would help them solve the case.
And remember they did not meet on US soil and maybe that was on purpose. Further, everyone thought he was dead anyway. He was packed off immobilized to Latveria. Even though Victor would be a strong suspect for the Ned's murder in the garage, they wouldn't have any proof. Now that doctor doing the exam is another story. I'm not sure if he was just knocked out or dead.
We didn't see the entire contents of that room so there could have been some equipment brought in for all we know.
I really think the General might have been a bit shady himself. In the comics, young Victor was recruited by the US to work on some projects for them. And we know in the first movie, that Von Doom had some defense contracts. So it's not such a stretch that he may have even had some shady dealings with General Hagar in the past.