Sorry for your loss.
I agree with your final paragraph, disagree in part with your second, and disagree with your first.
To the second: I don't doubt there's an implication of wrongdoing baked into the etymology of "committed suicide" - after all, suicide is a sin in Christianity and was historically a crime in England, and I imagine when the term first arose there was an intent for it to be condemnatory. But I think modern usage of the term is generally not understood to inherently carry that implication. IMO sometimes, as here, terms become established as first-class citizens in the language, speakers and listeners consequently don't even think about their etymology any more, and consequently the connotations logically implied by their etymology just cease to be salient to the vast majority of people.
(I also don't think the -cide suffix implies wrongdoing. Homicide is not necessarily illegal or wrong, and then of course there are words like "fungicide".)
But in any case if the term is to be eschewed, there are alternatives that avoid the implication of wrongdoing in the word "commit", are already well-established in the language (thus avoiding confusion about meaning) and avoid the new set of distasteful/offensive connotations that "died by suicide has". "Took his/her own life" is one; simply "killed himself/herself" is another. That is - we agree on your third paragraph, even if we disagree on details along the way.
To your first paragraph - I am perplexed. Did you (or anyone else) really just read this term for the first time (whenever you first came across it) and intuitively understand it was simply a new term for "killed themselves"? I struggle to imagine anyone grasping what the term was meant to mean without going to Google to figure out how it was meant to differ from the usual "committed suicide" (or either of the other less common but still well-established terms above); certainly I did not.