Putin couldn't let Ukrainians join the EU, start getting all the EU fund money and actually started living like Europeans. Russian population would see that at a large scale and start asking questions. He couldn't get back the influence over the country diplomatically so he resorted to terror.
Edit: I also wanted to add that this was the reason Putin and other Russian propagandists have been calling Ukrainians the brotherly nation (to show them how they care about them), the nazis (to show that their government is harmful) and that Ukraine doesn't even exist as a country (to show that they should all be the same people under the same borders).