You should neither discourage nor encourage hermiting. You should just let it be. What you have to look for is abusive use of alts or multiple accounts. If this were a relatively large production, sure, you could create some reasonable limits to the number of accounts any one person could snag, and I know a lot of f2p games that do just that (assuming that the accounts are all flagged "free" vs paid). It is, however, a technical and manpower hurdle that requires resources that may not be available.
EVE is a perfect example of a game where alts are highly discouraged as you can only train one character at a time. You can still get a lot of alts up (3 characters per account, need multiple accounts for more than that) and I had about 7 characters the last time I played regularly (love them PLEX...). However, that doesn't work in f2p where you can make as many accounts as you want (again, reason above for policing this).
Making characters choose one path or another only encourages alts, thus ending up at the same situation as currently exists, so changes to the development mechanics really doesn't do anything other than change the game for no net profit. However, it does make a hermit's life harder as not all hermits want to raise an army of alts to do things. (I kept 3 around in HnH: hunter, farmer, miner.)
The "skill synergy" doesn't really solve anything, either, and just creates other issues. You want to chop that tree faster? Attack the problem with more people and better tools. Encourage cooperative gameplay. Don't make "super characters" which are the bane of every PvP game. FYI, super characters don't discourage cooperative play. Cooperative play just makes getting super characters easier, thus if anything, it encourages cooperative play, usually at the cost of anyone else that doesn't have a super character.