And before you point out that Mono is not Microsoft-specific, my reasonable fear is that if Mono ever gets too effective, Microsoft can pull the rug out from under it at any point with patent claims on all sorts of pieces to .NET that might have found their way into Mono.
I'm happily only going to be working with computers until the end of May, 2015.
My reasonable assumption is that IIS will be unable to build a reputation as a "secure, stable, non-virus prone webserver" before it no longer matters to me (i.e. before the end of May 2015). Hence, it is in Microsoft's interest that Mono be as successful as it can be. Otherwise, .Net applications will only run on that part of the web market-share that runs IIS (never more than 30%). Another reasonable assumption of mine is that Microsoft doesn't want to be in any market where it has less than 1/3 the pie. So, while I accept your supposition that MSFT will ultimately find a way to kill Mono, I believe that MSFT will not be motivated to do such a thing until they can get enough people to trust IIS - which, as I say, I anticipate being sometime after May, 2015 :-)