If Wikisource's community discussed that issue thoroughly and agreed on the current way, then I guess its okay.
When you visit wikisource.org , you don't know that you can add content there. perhaps a little highlighting of what is going on the wiki is appropriate? also having a multi-lingual main page would be great too (introducing Wikisource with many languages)...
Dovi said that when the portal is on a wiki, it is much faster and easier to update..I agree with that..may be all of the other portals gets converted to mw installations? but comes the question..'the other installations wouldn't have sysops as there are nothing there except the main page, how it would be maintained?' a solution may say, make a sysop there from each language..
I am with incubating other languages on wikisource.org (sub-domain or as it is now) because as said, some languages will keep incubating till the end of time.
About the language approval and that any new sub-domain created should have mw completely localized, may be these unique languages don't have enough vocabulary to translate it? or don't have that contributors willing to create that vocabulary in the said language (yep, original research :P)..
btw I have sent this thread to fndn-l and ws-l but then I noticed that I haven't subscribed there ;)