I'm not sure exactly what you're trying to say when you say that the only valid reason for not signing Mookie is that the Sox did not want to pay him that much. I don't think any team wants to pay a player that much, but some do after weighing all the pros and cons. It's just not a cut and dry situation.
For a small market team, I can see an owner saying that he will not pay a player $350 million under any circumstances. Period.
For teams like the Red Sox, Yankees, and Dodgers, who are willing to spend a lot of money, it's not so simple. It's not a matter of either yes, we want to pay him that much or no, we don't want to pay him that much.
And the long term effect of such a contract is most certainly a valid consideration, no matter how much money the Sox have coming off the books in the next year or two. That's the type of contract that reduces payroll flexibility significantly for 12 years, not just the next few years.