Yeah, animation can be a bugger to transfer.
The main thing is the programmers you're working with simply do not have the time or do not WANT to program an export tool for Maya. They more than likely already had one for Max, hence their feelings that Max needs to be used.
My situation at work is very similar. Our export tools are Max-based, yet all the artists are using Maya. What we pretty much do is model and texture in Maya, port as obj to Max, and animation in Max. Then export.
Because all of the artists are using Maya, we're probably going to have the programmers make a maya exporter for us.
If your team doesn't have the time to do that, you'll just have to fit in with their workflow.
Max was THE game developer choice for a long time, mostly because Maya had been so expensive for so long. When Maya Complete (all you really nead for games) dropped to $2k, making it cheaper than Max/Character Studio, it started getting integrated more.
I'd estimate that most major studios use Maya, while the medium/small studios are about 50/50. Just my estimate anyway.
So, yeah, it's not that Maya CAN'T do the work, it's just that the exporter is made for Max and they don't want to make a Maya one.