I think loyalty matters in so far as it gets you upgrades for the ship. The last mission is more a matter of picking the right people for the jobs - if someone isn't loyal, I suspect they die in the crash when the part of the ship that didn't get their upgrade fails (but that's a guess).
Also, I doubt ME3 will be broken by specific characters dying in ME2. They've said that the only real problem is if Shepard dies at the end of the ME2, and that only means you can't load that savegame into ME3.
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"There's more truth in comedy than in tragedy." - Vanna Bonta
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