Windows will NOT recognize a larger-than-2TB disk without it being GPT - it is not simply a partition limitation.  At this point, there is no way to remove the disk from the array, so you will have to do a backup/restore to a newly-configured, smaller array ... or add another new disk(s) and configure a new array (each array is seen by the OS as a separate "disk"), losing availability of one disk but saving the downtime and headache of a backup/restore.  
I have a PowerEdge 2900 with PERC6/i controller. Originally it had four 500GB disks in RAID 5 MFT split between system and data.  About a year ago I added a 500GB disk and extended the data partition. Now the data partition is getting full again so I want to add another disk.  Since it's not a GPT disk (the BIOS won't boot from a GPT disk) I can't extend the data partition beyond 2 TB but I can live with that by shuffling stuff around with a third partition. So I put in another 500 GB disk and went through the same procedure I did last time. Now when I look at the virtual disk in Dell Server Manager it lists it as 2,326.25GB and if I select Reconfigure it shows all six physical disks as being part of the array. But in Disk Management (Small Business Server 2008 Standard) I don't see any unallocated space; just a 125.65GB system partition and a 1735.29GB data partition. Where's my unallocated space?
New disk not seen in Disk Management