I have the same problems but i have made a solution.
1. I bought a 200 Gb USB drive
2. I installed OS Mountain Lion on it (http://getintopc.com/softwares/operating-systems/mac-os-x-mountain-lion-free-dow nload/) AND I've copied iWeb from the internal Macintosh HDD to this External disk also
3. When I start my iMac (mid 2010), I push the Alt button, when the chimes comes.
4. After a few seconds there will by a booting menu
5. I choose OS Mountain Lion on the external disk
6. Then I copy the iWeb Domain file (domain.sites2) from the internal Macintosh HDD to this External disk
7. Then I start iWeb and now I can edit and upload in the old fashion way.
When i have to make changes in my websites i do it under OS X El Capitain.
When I finish editting I reboot with the external disk and copy the iweb domain.sites2 files from the Macintosh HD to the external HDD, upload my website and thats it.
Works fine.