I think the point people are trying to make when they say this is that even the most avid of Halo fans probably don't want to make Halo for their entire career and the structure of 343 (and MGS in general really) doesn't offer a great deal of creative freedom outside of their major tent pole franchises.
So while they will be fine in the short term there is a real risk of attrition and losing talent as time goes on and there's nothing for these individuals who've had there fill to do within MGS, except move on to Gears. Then, as the Halo brand becomes less interesting as time goes on there will be less new blood to keep the franchise fresh.
This is my feeling, at least, and it's my biggest gripe with Microsoft making studios named after their respective series - eventually the creative talent will dry up and there's no other outlets for them at Microsoft at the moment.
If those people want to make new IP they can leave.
They didn't just name 343i after a Halo character. All 343i does it work on Halo games and other Halo stuff. People don't go there to make other stuff and if you did then that person is naive.
People need to get over the fact that 343i will make Halo until the day Microsoft closes them down.