The restriction is contractual in nature, and contracts are enforced by the courts system through civil litigation. The courts
can overturn the contract on antitrust grounds,
but that will never actually happen at scale, due to a set of interconnecting reasons:
1. Courts do not consider hypotheticals. In order to get the issue before a court, you have to actually buy the land and actually get sued over it.
2. Most people in a position to start up new grocery stores barely have enough capital to start one store, and cannot afford to tie it up in litigation for the next five to ten years.
3. Those in a position to attack the deed restriction are other large chains, who all have class solidarity and would never dare of attacking their own business practices.
Sometimes the logic behind #3 breaks - usually when a business in one industry tries to expand horizontally into other industries. This used to be a lot more common back when we had functioning caps on business consolidation, but now pretty much everyone owns everyone else. And sometimes someone decides to commit financial suicide, breaking the logic behind #2. But that brings us to the next reason:
4. Courts really, really do not like getting people out of contracts, even - and especially - really, really unfair ones.
Because...
0. Courts do not want to be arbiters of fairness, because fairness is arbitrary. Laws and contracts carry the illusion of impartiality, which is often good enough to trick otherwise bright minds into getting lost in the weeds of caselaw and clauses instead of asking "Hey, aren't we playing into someone else's hands"?