It is not money, it is YEPs. "Your Elite Points"
They come with rules attached, just as any medium of exchange does. For instance, the government requires you to pay taxes: they are telling you what to do with your "hard earned money". Other examples abound. Every institution has rules that govern how to deal with whatever the medium of exchange is.
A bit of history: those of us that founded Elite came out of the "cases" system, which used "Ladderbux". One of the major beefs with Cases was that their ladderbux system was meaningless. They were subject to hyperinflation, they got worthg less and less every month because they were essentially "printing money" for premium members.
Two of our main goals when Elite was created were to institute a "currency" that had measurable value (which YEPs do) and a rating system that was fair and "cheat-proof" (which ours is closer to being than any we have seen elsewhere).
As part of this process we decided we would NOT have a "ladder", where your rating depends on WHO you can make a match against, and would go with a tournament-only league. This worked very well except for one thing: our players complained they had no "official" way to play matches with other Eliters, between tourneys and/or for bragging rights. Many players asked if we could create a system where they could WAGER their YEPs on head-to-head competition.
Thus, the mini-tourneys were created. However, eventually another problem came to light: since there was no rule against it, strictly speaking, some of the richer players began overtly using mini-tourneys as a means of transferring YEPs to their poorer friends.
Now this is not, in and of itself, such a bad thing, BUT: the thrown matches have an effect on the players' ratings, albeit a small one, and many of our players began complaining because they saw this "throwing" of matches as being unethical and dishonest.
Since Elite, first and foremost, is founded on integrity and fairness, we couldn't allow this to continue. We'd sooner get rid of the minis altogether than allow people to manipulate them like that. Since it is not possible for a TD to monitor every mini s/he creates for the full length of the match, there is effectively no way to police this.
The best solution we could come up with is what we are trying now: the requiring of sufficient stakes to make the loss of the mini not be a grave financial bombshell.
I hope this helps you understand the genesis of the rule, and perhaps reevaluate your objections to it.