The mortgages may be junk in terms of collecting payments, but the underlying asset still exists (the homes) so I wouldn't characterize these as junk, necessarily. It doesn't strike me as unreasonable to assume that if people had the cash for their monthly payments, they'd want to keep their homes, so if there is any kind of upturn soon, I'd expect to see mortgage defaults drop quite rapidly. The system just isn't functioning right now, so no financial asset (mortgages, stocks, bonds, you name it) is being valued at anything near normal levels.
You can certainly blend different valuation methods to attempt to capture both present value and discounted present value of future cash flows etc - research analysts do it all the time! The problem is in convincing anyone else that your method is more valid than anyone else's. Most methods will appear more valid in some financial conditions than others, and of course, as soon as any new standard is set, new financial products will very quickly emerge to exploit it (i.e. that will look better than it otherwise would under the new accounting status quo). Mark-to-market was initially incredibly painful for most firms (not just financial ones), but eventually it became part of the system, and it failed to prevent abuses.
