That's actually one of the reasons the president has a veto. If the president doesn't want the law to pass, then there isn't much point in passing it unless Congress makes a show of force with the 2/3rds majority, which is also the majority needed to remove him from office.

Similarly, one of the reasons the president has a pardon power is because he doesn't have to enforce those federal offenses. E.g. imagine that a president without pardon power instead offers "plea deals"/settlements for a $1 fine or concocts vacuously lenient house arrest enforcement.

The original constitution basically accepts that there is very little you can make a president do, and it instead formalizes what would otherwise be a gray area (it does have plenty about what he can't do). Some of this has changed over time especially as the judicial branch has granted itself more power.