1. Those are independent decisions. We know this because rebuilding teams are not lowering ticket prices in 100% correlation with how they slash payroll. Businesses want to maximize profit - so they will charge prices and pay labor in an effort to do that. Now sports teams are a little different since they are often vanity purchases for dudes who are already loaded, but the general principle holds. The team charges that $1000 because they can, period.
2. So - since the money is going into the baseball economy from us (and TV advertisers principally), the question is why is not spending money in free agency or whatever a bad thing?
2a. I like baseball. That means I like baseball players playing baseball games. If the players are getting a smaller cut than players in other major team sports - that makes them unhappy and increases the probability of some kind of labor stoppage. I don't like less baseball. Now, I don't think a strike is inevitable. But the owners have time to get out ahead of this and it would be very smart of them to do so.
2b. Transactions are cool! I think of ESPN having free agency specials for the NFL and NBA. The NFL in May - when nobody should be thinking about football - gets a weekend of serious coverage to itself because of the draft. The winter meetings were baseball's chance to market itself in the offseason. The current system is depressing that, which lowers year around interest in the game ... which is bad.
2c. Related to 2b. Talking about awesome players in the offseason is cool. Having franchise cornerstones be available in free agency makes baseball more fun to follow 12 months a year. The game already does a crappy job celebrating the current players and product (see how joyless the national broadcasters are!). This does not help.
2d. More teams should be trying to win - that is why we root for teams. Too few teams are doing that - while a five year rebuild is RATIONAL, this is an entertainment business, and that is not good entertainment.