Initially it likely will have some growing pains but by 2009 most of those should be in the past. Security for the platform may be a bigger problem, but with attacks moving to the application layer and services like Google becoming the next big security exposure, as a result, this might actually not matter very much.
Because it is a contained hardware/software offering and will represent a much deeper collaboration between Intel and Apple, this may actually make better use of some hardware, like hybrid drives, than Vista currently does (though Windows 2010 will likely reverse this).
There are likely two long term problems. The first is the inability to competitively bid hardware, given there is only one hardware vendor pre-loading the MacOS. The second is with Windows-Mac compatibility so high, software vendors who support both Windows and the Mac may drop Mac support to contain costs and assume their Windows offerings will run on the Mac. That last, at least from an IT perspective, might be a good thing, and go a long way to addressing the first problem as well because, if you can keep the applications stack basically constant you can competitively bid Apple in the years after the initial bid is won.
The short term problem is trust. Apple abandoned this market some time ago and refuses to share roadmaps with IT buyers, something they expect to get from any hardware vendor they deal with. This makes it difficult for them to trust the companys commitment to them and this will probably stand in the way of success.
They will be at their strongest during 2008. And if they can increase market share dramatically they are still around 4% right now they should be able to carry that momentum into 2009 to go head to head with Windows 2010 (probably mostly in small to medium business but this will be an interesting battle to watch regardless).
However, if share remains below 5% after this push they will likely conclude that their resources are better spent with CE products going forward, where a lot less effort has made them much more successful. This could mark the beginning of a new more powerful Apple, or the final move after the firm took Computer out of their name.