Short answer: YES!
My take on this situation is as follows:
1. Microsoft has already been bitten once having to support multiple architectures (see Alpha and MIPS), and to avoid this problem in the future (see x86-64 and IA-64) they hace created .NET as a platform neutral environment.
Unless .NET can run a great deal faster than Java, then this is a very risky strategy. A port of Linux to x86-64/IA-64 would allow developers to create native applications (open office) that would run rings around .NET applications compiled to CLR.
There's no reason to expect that CIL code /can't/ run at the same speed as Java bytecode. They're the same basic concept, just a different implementation.
Where it might fall down is in the implementation of the VM and the crap added to CIL to support various "look how much better than Java we are" features.
Oh, and Java isn't 'native' at all, just in case you were confused about that. Where Linux wins is that a huge amount of source code is available to allow you to recompile your favorite applications on a new platform, without having to wait for the author to release a platform-specific variant. If the source /isn't/ available, you still have to wait.
-- Corey Murtagh The Electric Monk "Quidquid latine dictum sit, altum viditur!"
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