I have never been in a keeper league, but I will throw in my two-cents...
<b>The Potential Problem...</b>is that the team giving up the draft pick or the team giving up the marquee player for next season may put their 'franchise' at a disadvantage going into next season. If that happens, the fear as a commish may be that one of the two coaches may quite instead of put money down on a season they most likely will not win. Consequently replacing the owner of that 'franchise' will also be difficult for the same reason.
<b>My Recommended Solution...</b> would be to explain these dynamics to the coaches involved. Point out how they could potentially damage their franchises (and the balance of the league) for the particular year of the draft picks. I would be clear that the potential risk will be gathering future moneys for a franchise that could be at a distinct disadvantage for the year. I would insist the two owners involved pay their league fees for those seasons affected now (before the trade) to ensure the moneys for those franchises in case something goes terribly wrong.
<b>The Worse Case Scenario...</b>would be one franchise being screwed in the long term because a player got hurt or a draft pick got hurt. One of the following cases will happen:
(a) The current owner of the dismal franchise can then choose to quit and not get his money back. Getting another owner to take over the franchise with its league fees already paid would be easy.
(b) The current owner of the dismal franchise can decide he still wants to manage the team even though it is at a disadvantage because he has already invested the money into it.
<b>The Actual Rule Should read...</b>Any franchise acquiring or sacrificing a draft pick must pay league fees for that respective year(s). If a team trades its #1 draft picks for the next two seasons, both teams involved in the trade need to pay league fees upfront for both of those seasons before the trade is approved.