Here's a spit ball. Somebody mentioned it earlier in the season, but I think it's worth revisiting.
Pat Willis' cap number is $8.3 mil for 2015 and $9.6 mil for 2016. Dead cap in either year is under $1 mil.
The 49er's current cap number for 2015 is about $150 mil; they'll need to do some veteran offloading. Willis would be a prime candidate given Borland's play and Willis' low dead cap.
The 49ers will try trade him to a team with cap space that would find the zero guarantees and very low dead cap risk attractive. As trades go in the NFL, it wouldn't cost much in the way of a draft pick.
It doesn't look like his toe injury is that serious...banged up from repeated strains and sprains. A chronic turf toe might be more problematic. In any event, the low dead cap makes it a low risk proposition.
This deal would free up the first round pick for any number of possibilities: the NT that's needed now; a cover corner backup to complement Shields and House (or compete with House) if Williams is not re-signed; an OT if they can't come to terms with Bulaga; an OLB replacement for Peppers come 2016.
It opens up more positions among which to choose the best player available, rather than a forced pick to fill a glaring need as we've seen in the last 4 drafts.
SF will ask for a 3rd. round pick; Thompson will offer a 6th.; Willis will go elsewhere.