WellÉ
There is no logical/practical reason to take it out. None.
It isn't milspec: So what, who cares if ONE weapon in the Inf arsenal isn't milspec. It's not like there's a written in stone law that says you can't include a non-milspec weapon.
You just should because I think so: I've been told mine's a subjective opinion
And further the more why would anyone in their right mind want to decrease the variety of weapons in a mod regardless of reasonsÉother than balance, that for which the Desert Eagle posses no context for removal.
IMO it's the best looking skin of any weapon I've seen in Unreal Tournament. Whoever skinned the DEagle did the best skinning job I can remember, just look at these and tell me which is the best:
First up, Infiltrations Desert Eagle:
Second Tactical Ops Desert Eagle:
Thirdly Strike Forces Desert Eagle:
Fourthly Counter-Strikes Desert Eagle:
Fifthly Firearms Desert Eagle:
And yes, even though some of them are good, none of them have the detail that Infiltrations does.