Unfortunately, the WS-Fed PRP protocol specifies that you must treat wctx as an opaque identifier at the fed server and may only pass it through unchanged. Thus, when this patch went out, it broke you.
Unfortunately, the protocol is not designed so that you know anything other than what's in wreply or wtrealm to make a decision on. If you wanted to have "original URL" context information from the protected app, you would need to find a different way to provide that such as a "domain-wide" cookie issued by the app that the fed server would "see" in the request sent to the fed server. I could imagine you might run into problems with something like that as well, but it seems like your only good option other than having the app set up as multiple different apps (different wreply).
Best luck figuring something out. The patch has been "interesting" for sure. We are still working through some issues internally similar to this.