I still think the Protheans were awesome and self sacrificing. Sure they told their VI to shut them down... and he did. He was a VI, not an AI - I didn't get the impression he was making decisions himself, he had been given a list of priorities and was devising the best course of action to fulfil those priorities, but it was the VI's creators, those Prothean scientists, who decided that the project came before the race's survival.
You don't have to believe that if you don't want to... but if the Protheans didn't make that decision consciously, then they were unrealistically dumb.
As an organic, if I could get people to FREAKING BELIEVE ME about the reapers, one of the things I'd do is build and send out some Ark ships to find planets that are a few years away from Mass Relays, and build sleeper colonies there. Wipe all ship vectors from my database as soon as they're off, send 'em in different directions, have them not communicate in case of indoctrination. Hell, maybe even build a generation ship or two. That's what we used to think we'd have to do if we wanted to colonize stars, before we discovered FTL travel - Ark up some ark ships.
The Reapers can't (and obviously, based in Ilos, don't) check every single system. They check ones that have Mass Relays, and all the ones that are a reasonable distance away from Mass Relays. So get some volunteers, Make some Ark ships, and tell them not to come back for a few thousand years. It's do-able. And if we could technically do it, why couldn't the Protheans? They seem to have been significantly more technologically advanced than we were.
Now, we can't be sure the Protheans didn't attempt this, and fail. But the resources used to found Ilos could have been used for another colony attempt, or an arc ship, or something that would have given them a chance at survival. They decided to spend those resources on the conduit project instead, and that says something... to me anyway.