I'm afraid this is not something we're currently working on right now. I hope that we can look at this further at some point in the next 3-6 months, but I'm afraid I can't provide any guarantees.
We do have a fairly low maintenance solution at the moment for CIS contractors (see here for more details), this involves posting your gross sub-contractor payments to a holdings account, then when the NET payment leaves your bank account this is tagged as a transfer to the CIS holdings account. This allows you to conveniently track any CIS related liabilities.
I doubt that we'll go down the route of offering a check box as it requires a significant overhaul of some underlying systems to make that work. We will however seek to extend the reporting side and possibly allow CIS returns to be delivered electronically to HMRC.