Are you talking about the current war, or do you mean that they were there before Russia took Crimea in 2014?
If you mean they were there after 2014, what does that matter, it was still stolen land at that time.
If they were there before 2014, I would agree that some form of a path towards citizenship should be made, but again that is Ukraine's prerogative.
Edit: Reading your second article, that is exactly what Ukraine is proposing, expelling Russians who moved to annexed land after 2014. What about that seems unreasonable? They took a gamble and moved to a conflicted territory, maybe they were led to believe it was their right, but it doesn't change the reality that it wasn't.
That does seem like a troubling situation. I do imagine that there are likely quite a few people who took those positions with good intentions, but when the new ruler comes to town and asks who wants power, it does seem obvious that there are strings attached. In this case, the deal was indeed to become a traitor in exchange for power/position, but I'm sure many were signing up just to survive.
You're right, there are probably good people that are going to be harmed alongside the bad, and I don't think there is a perfect solution. I would say it needs to get talked about as we get closer to a peace deal, it's truly regrettable that Russia decided to create this problem, maybe they could also work towards a solution for these citizens they forced into this role.
Edit: purely hypothetical, but one thought comes to mind. A compromise might be acceptable if they were given the choice to either retain their Ukrainian citizenship, but lose their position, or to defect to Russia. Though, once again this realm of decision making lies entirely in the hands of the victor of the war.