I would worry about keeping him alive through the combat if challenged, but I suppose you could do so by directing challenges to the stealth team's leader.
There are 4 ways to improve the odds of your commander surviving a challenge.
1) Promote to Shas'o. This gives them 4 separate stat increases that improves their survivability in combat. Improved weapon skill means that fewer hits will actually land, an extra wound is significant in the fact that you can probably count the number of models on one hand that have 4 wounds or more and aren't monstrous creatures, you get another attack, and you get increased leadership, should your unit lose the combat.
2) Shield Generator. Yes, you're sacrificing one of your weapon hardpoints, but if you're expecting your commander to get involved in melee (and especially challenges) then it's a wise investment.
3) Stimulant Injectors. Yes, FNP got nerfed down to 5+, but it also affects a much wider variety of wounds. All in all, I believe the stimulant injector is still worth the same amount of points.
4) Iridium Armour. Yes, it slows you down incredibly, but now those pesky power weapons won't be hurting you nearly as often. Besides, if you're using the Vectored Retros then you're going to be getting most of your movement from that anyways.
This doesn't necessarily mean that you have to take them all together, just letting you know what your options are.