Most of the anti-Microsoft sentiment I've seen relates to things that happened years ago under different leadership. In recent years they've really pushed interoperability and open source. It's not so strange with that lens.
I also think many people would have been upset no matter who acquired Github (nobody's good enough for FOSS's darling). But it wasn't turning a profit and $350m is a lot of investment to carry. The acquisition gives people their pay day and provides Github a pretty reliable base for the future.
I don't know what they'll change. I suspect we'll see more integration with other MS products and tools; it'll be interesting to see if they change the UI. Maybe they'll go for something bigger like a cloud-based VS Code + Github offering... that'd be pretty cool.