I'll take a stab at an answer while trying to remain as factual and apolitical as this subject can be.
I don't know that there's a clear answer, but there are a few facts to consider. Rick Perry stated that he wanted to essentially shut down the DOE during his presidential campaign and has opposed some of the alternative energy loans in the past. He can't exactly pull the plug on everything as the head of the DOE, since congress authorizes the programs, but he can influence which programs get priority and act as a roadblock for the programs he doesn't like. As far as I'm aware, he has not commented on the ATVM specifically, but it seems to fit better with the pro-jobs and pro-oil stances Perry has historically espoused since it does not specifically target alternative energy or fuels.
My speculation on what that means:
It stands to reason that the ATVM is not likely to be specifically targeted and will only be negatively affected if the entire loan program office is effectively stalled. That could play favorably for EM, if the office sees an opportunity to ingratiate themselves with the new boss by issuing a loan to a company that fits his politics. It could also cause them to be fearful of granting any loans. I think it would help substantially if there were some positive statements about the Elio by Perry, but as far as I'm aware, he hasn't made any (positive or otherwise).