That would be the cleanest way, but at the end of the day what you're doing is creating yet another Linux distribution. It's unlikely we'd ever have the ports coverage that would allow users to just install the ports version of whatever Linux software they want.I had another idea in the past: Don't repackage anything, instead bootstrap a GNU toolchain targeting Linux in some "linux-base" port and use that to build existing ports in a Linux variation for installation in /compat/linux. This also sounds simple at first, but is probably even MORE work in practice ... but it would come with the advantage that you could somewhat quickly add e.g. libraries missing from our Linux userland based on existing FreeBSD ports ... If only I had the time to at least attempt some proof of concept for this ...
This is why I agree with kpedersen that we need coverage for the two predominant Linux package formats, RPM and Deb. Maybe just a lightweight Deb distro with Alien would be enough.