I haven't kept up with the MLB signing rules, but here is a Wikipedia entry supposedly under the current CBA:
"A player who is eligible to be selected and is passed over by every club becomes a free agent and may sign with any club, up until one week before the next draft, or until the player enters, or returns to, a four-year college full-time or enters, or returns to, a junior college. In the one-week period before any draft, which is called the "closed period", the general rule is that no club may sign a new player."
The way I read this is that an undrafted college player can be signed as a FA. A coach removing any scholarship will - if the player is pro quality - lose the player to FA.
Most - like overwhelming majority of drafted juniors - know that their bonus negotiating leverage evaporates if they don't sign and wait until senior year. So, while there may be a few willing to take the 2k senior bonus instead of a higher junior year bonus, the overwhelming majority will take the junior year draft bonus.
So, an undrafted junior (now a rising senior) can sign as a FA until school begins; a drafted junior recognizes that the largest bonus (plus the MLB scholarship) strongly incentives him to sign the draft contract.
I see virtually no scenario where the withdrawal of the senior year scholarship results in that player staying at that school. In such a scenario, the coach is essentially cutting the player.