You do make some very good points and I think your last paragraph sums up how I feel about the situation. They aren't in the same position they were and they don't have any type of strangle hold on where the computer industry is heading. One of my closest friends owns an embedded software company and almost everything they do is *NIX based. Embedded systems still require speed which usually translates to ANSI C and that is still platform independant.
I wouldn't argure that Microsoft won't try their usual tactics, but I think keeping Perl intact works to their benifit. It looks like their goal is to make the .NET platform too attractive to pass up, and keeping Perl "Perl" will encourage people to make the move. But then I'd guess they'd try to convert people to their languages.. just like they're doing with Windows Script Host. Of course I can't find a link to it now, but in an article I read about WSH, they talk about how Perl is a "great" language, but feel that VBScript is a better language under WSH. I'm sure we'll see the same thing with .NET