There have been a lot of unfavorable stories about MS on HN, including recently. We don't do anything special to penalize them, nor do we let users abuse flagging in the way you suggest. In fact the Windows 10 update nagware saga has appeared numerous times on HN's front page, including multiple stories about clicking 'x' on the dialog box, how it screwed some African satellite operators, etc. The current one fell suddenly off the front page because of software (it set off the flamewar detector).
If MS "infiltrated" HN, it's news to me and I'd like to know about it. It's our job to protect the integrity of this place for the community and we take it seriously. When we see gaming and manipulation we crack down on it hard. But actually the BigCos aren't the ones who do such things. They're (rightly) too risk-averse.
If you think you see evidence of manipulation you should email us at hn@ycombinator.com. When we get emails like that we always look into it.