I would really need to see some examples of that. Adobe doesn't deal well with Linux (or anything non-Windows) and Microsoft would make more money with Linux around.
Perhaps you think that but I don't think they are or their shareholders see it that way. Microsoft tends to only deal with Linux or the open source world in an effort to avoid criticism. In fact, that's just too ironic of a statement and I think needs a little justification.
Why wouldn't they? What would be the benefit of offering Flash for Linux, or Mac OS for that matter? Actually, why would they make a Flash plug-in for any browser other than IE? It seems to me that a reasonable thing for Microsoft to do, after acquiring Adobe, would be to discontinue Flash support for any OS other than their own, and to stop making plug-ins for other browsers, which would help IE regain some (if not all) of the market share it's recently been losing.
I may be paranoid, but it seems quite plausible to me that Silverlight is merely another example of Microsoft's famous "Embrace, extend and extinguish" strategy. Since Silverlight failed to gain wide acceptance on the web (well, certainly not as wide as Flash), acquiring Adobe to get hold of Flash would enable them to skip the part where their software first needs to be accepted by a significant majority of users and allow them to skip right to phase two, which is concentrating more and more on how Flash works on Windows and IE, leaving other platforms and browsers behind. Truth be told, Adobe has also been known to concentrate more on how their plug-in works on Windows than on other platforms, which meant that Flash would usually perform far better on Windows than on Mac OS or Linux.
Because Firefox is reaching 50% of the browser market (I recently read that somewhere on HN) and if they make it IE-only, content producers are going to stop using flash.
I really do think all product development for Linux or Android would be cancelled (Flash for Windows Phone 7 only).