Throwing in the towel for a season and "building for the future", or mortgaging the future and pushing it all in for a chance at winning the title this season are completely legitimate strategies in both fantasy and real baseball... and one of the reasons why playing long-term keeper leagues is so cool.
However, there is some drawbacks to that... unlike in real baseball, franchises don't have "values" that are associated with them (or if they do, all the teams in a league are relatively the same). If you can walk away from a team at any time it no longer suits you, there's no reason not to trade away your future. The concept of "mortgaging the future" only applies if you have a future that you're tied to (either with money or ownership). If the league's future is uncertain, or an owner can bail on a team anytime they want without repercussions, that future value becomes a lot less (and owners building for that future should take that into account and demand more for their current players).
Solutions? There aren't any real good ones... Having people "buy" franchises for long-term (paying dues many years in advance) is never going to happen, and penalties for players leaving a deadbeat franchise aren't likely to be paid. For all intents and purposes a franchises "value" is made up of 80% this season, 18% next season, and as little as 2% beyond that. Any owner who's making moves with chips that far out in the future is playing with fire.
If you have to make a rule for your league, beyond just making owners aware of the fragility of their team's value and the value of future picks, I suppose you could put some kind of restrictions on owners. For instance:
1.) All owners must pay half of next year's dues at the ASB. Failure to play the following season forfiets that money. No assets beyond next season may be traded.
2.) You're not allowed to trade assets for draft years until both parties have paid that year's dues. This way at least the owners involved would recognize that they are trading something of legitimate value. If they want to trade (for or against) assets in the distant future, they need to be paid for. If they no longer own the team at that point, the dues for that season will be an incentive for a new owner to take over that disadvantaged team.
and (if you're playing with a more involved model)
3.) Player contracts are contracts with the league. If you're signing a keeper to a four year deal, money needs to be set aside to pay for that contract (or at least some portion of that contract). It's not fair to future owners of a team to be saddled with contracts that they didn't agree to. Likewise, it's not fair to those owners to lose out on good contracts simply because the previous owner was irresponsible. At least some part of the value of the franchise needs to be tangible. If an owner leaving is going to leave a black-hole in the league, and no sane owner would want to take over that orphaned team, you're in a real tough spot as the commissioner.