The "Make My Monster Grow" trope is in full effect

It is a well known established fact, that whenever a huge enemy appears, it will ALWAYS have a glaringly obvious weak point that is very shootable.

Alternatively, just open a huge portal to a Daemon World, in Warhammer 40k. No sue is going to be able to last more than a few minutes, tops, on one of those. I don't care what kind of mecha you're driving, several billion daemons, coupled with the laws of physics (or lack thereof) will annihilate anything. Best part is that, as long as the agents keep their heads down, their SEP fields will keep them alive (Maybe) long enough to make sure.

Upstairs might not like it, but until they get the PPC some mecha-killing weapons, they should just be glad there's a way to dispose of sues like this at all.

I think that, in theory, an APD division specialising in a mecha continuum such as Gundam would be equipped with the proper tech (However, there is no such APD division — yet). Otherwise, Floaters' Special Operations Division or the Eclectic Subdivision of Advanced Species spring to mind.

That said (and like what VM said): I reckon the agents would just take the Sue out before she got into her Mecha. Makes everything so much simpler.

However, I'd be careful assuming that just because the Sue is in a mecha, the agents would need to be in one as well - an agent specializing in such a 'verse would be just as likely, I think, to bypass the Epic Mecha Battle and make handy use of a blowtorch and a wrench to disarm the Sue before dispatching them.