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Upgrade 2003 Domain/AD to 2008R2 Recommendations

We currently have 2 domain controllers running Server 2003 x64.  Roles include AD, DHCP, DNS just regular Domain Controllers.  I am wanting to upgrade both servers to 2008R2.  What would be the best plan to get these upgraded?  I would like to avoid fresh installs on both servers since availability is critical since we are an active hospital open 24/7 and cannot have the servers offline for too long.  I have heard in place upgrades are also not the best way to go since there can be quite a bit of cleanup after the upgrade is complete?  Should I take down the secondary DC, run soley on server 1 while I do a fresh install on server 2.  Once server 2 is ready to go, dcpromo it migrate everything from server1 to it and then take down server 1 for a fresh install and then dc promo it back and pull the roles back from server 2?  Which would leave us running a single DC server at all times?  The tricky part I forgot to mention is that server1 is also a file server for all AD users home directories which would mean transferring all network resources over to server 2 and modifying the group policy to redirect the workstations where to locate mapped drives, etc.  I do have a virtual environment that I could try to transfer the physical hardware to a vm environment temporarily while the physical servers get upgraded and then transfer from vm back to physical using dc promo and other migration techniques? Any suggestions would be much appreciated.  I would like to hear that inplace upgrades are safe but there are alot of admins recommending against this approach.
2 Solutions
Some of my preferences:
1. Never use domain controllers for other purposes
2. Fresh installation of any server

Therefore you might want to consider creating a VM to act as your file server and this will free you from deciding whether to fresh install or in-place upgrade. I would usually do a fresh installation.
Darius GhassemCommented:
I would not do a in place upgrade you need to do a clean install which is the safest cleanest way.

I would demote DC2 then do a clean install on this server to get Windows 2008 Server R2 as a DC like you suggested. Once you have done this do the same with DC1. You can use Robocopy to copy data over to DC2 if you would like to do this.
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