You can use Quicktime Conversion to create a DV25 or DVCPro50 AVI. Those may only work if your compressionist has the appropriate codec installed.
I've sent DV25 .mov files to a Windows box for encoding but there is a 2GB source file size limit but that may depend on his compression app.
As Koz points out it, a lot depends on what codes is inside that .mov.
Episode and probably a few other Mac compression apps (MPEGStreamclip?) may be able to convert your source to .avi but again even that may depend on what the avi wraps.
If you need to got the .wmv route I'd suggest using 1 Pass VBR with a very high Quality setting (even 100 if you can handle the large file). You can do this in Flip4Mac (which can also work inside Squeeze and Cleaner as well as Compressor) or Episode.
Maybe a very high data rate MPEG2 Program Stream might work too. I've used that to distribute broadcast spots through DGFastchannel.
If your web designer can give you the encode specs (data rate, frame rate, frame size), why not create the FLV file yourself which they can then integrate into the web page.