Hmm... I'm not sure if this means that choices involving squadmates are a problem , or that the trilogy structure itself is a problem.
I think it's more of 'choices to kill a squadmate.' When death is optional... the plot has to be designed on the assumption that it occurs, even if it hasn't.
Death choices need to be stepped down a bit- there are plenty of other delimmas and branches that are less extreme and easier to reflect while moving a character forward- or there needs to be an inevitable break between the PC and the NPC regardless/as a consequence.
In SWTOR's Trooper Story, there's a NPC named SGT Jaxo (IIRC). She's a major supporting NPC/flirtatious love interest. There's a point later on where she's stuck on a station about to blow in a delimma of 'save her or save numerous other POWS.' She begs you to save her, afraid to die. If you don't, then she dies- but if you do, she's so distraught and haunted by guilt that she breaks up with you regardless.
I don't necessarily think that's the strongest of writings- I suspect that, were it a Companion, a lot of players would feel betrayed and meta-game/rationalize letting her die to save the many- but that's an example of how a character death choice can be managed.
Personally, I'd rather more choices like Garrus's ME1 development, where you push them this way or that ideologically- and then follow those choices. Let ME2 Garrus be at Omega as either an undercover C-SEC cop, or a Spectre. Let Garrus adopt approving/disapproving tones of choices based on his P/R slant, rather than make him the always supportive buddy.
Mordin's Loyalty Mission was also a good example of a choice that had important character implications further down the line- even pushing off whether it affected his survival or not, rather than cast it in those terms.
My personal ideal standard for choices is that they be less about divergence, and more about approaching the same things later on from different angles. Given Bioware's structure, divergence is never going to be a reality- so having mutually exclusive choices that have to be either watered down and equivicated, or simply run away from, really just undermines the premise. Might as well go in a similar path from the start, with a tone change by design rather than de facto reality.
My favorite Bioware choices, at least in concept, have been DA2's ending and the Mage/Templar recruitment choice in DAI. Both choices lead to pretty much the same things- but by changing the tone, and only minor gameplay changes, you change the meaning and impression of those things. Hawke as the symbol of the Kirkwall Annullment- it wasn't carried forward to my satisfaction, but being the hero of one side or the other of a war that was already going on had potential! Likewise, the difference in Red Templars/Venatori gave more feeling for the DAI epilogue slides, which suggested different (but similar) ending states for the post-Inquisition power structure. Whether the Templars remained, or were folded into the Inquistion, or became a new organization... the same functions existed politically, but name changes suggested a distinction larger than was.
That, in my mind, is better than making a major distinction from the start, and then walking back on it.