Yeah. Not may groups have any real beef against IE as an organization (though individual members and, as Weirdo said, certain expeditions can cause friction on a case-by-case basis). Otherwise, I honestly haven't really seen much of them past the post-Jihad wrap-up reports (see ISP3). They've survived by a mix of mostly just being an impartial archaeological group that usually plays by the book, and being generally irrelevant to the plot ever since the last Jihad plot threads were either wrapped up or put into cold storage.
The only real way I can see the organization as a whole becoming relevant (and potentially under threat) again is if either
A: some IE explorer has the great idea to go off the beaten path on a totally-not-ill-advisable trip to check out what the Homeworlds are up to,
B: a WoB Shadow Divison or Hidden World pops back up, or
C: one of the big factions needs a big shake-up, so IE conveniently finds some Earth-shaking lost historical records that throws the legitimacy of one of the reigning dynasties or blood houses into doubt.