I see choosing to explore on one's own not as "losing" power and resources, but more as not gaining power and resources as quickly as someone who groups more often. Seen this way, soloing is not so much a punishment as a conscious tradeoff.
All that said, two more points on soloing. First, it might be useful to reiterate the observation that nobody really solos in a massively multiplayer online game -- you just interact indirectly with other players, rather than directly. When you leave messages describing what you've seen while you were out exploring, or buy or sell from a Bazaar or Auction House, you're actively participating in the game. The fact that it's not direct interaction with strangers doesn't make it any less valuable to the other players in the game. It's still a useful form of contribution; it's another way to be part of the community of players.
Second, although I prefer solo play myself, and hope that there's some of that in a Star Trek MMORPG, I acknowledge that for it to feel like Star Trek, the group play experience is absolutely required. Whether on a ship or on an away mission, nobody in Star Trek is truly on their own -- they're part of a team, almost a family. That's always been part of the storyline of Star Trek, and an online Star Trek won't feel right if it's designed to be too soloable.
So while I personally prefer not to have my success depend on other people honoring their commitments (I hated being given group assignments back in school :) ), I can't imagine ST:O feeling right without being designed to encourage and reward grouping.
It would be amazing, and satisfying beyond words, if Star Trek Online could be designed such that the Barclays of the world could be made to feel welcome and useful in a pick-up group heading off to run a mission.
That would not only be true to the spirit of Star Trek, I think it would produce a very good game.