Yeah the idea behind a pardon is that the head executive is basically saying that you’ve been punished enough and that no further prosecution will occur. It’s similar to how they can stay a death penalty. But the big downside is that accepting a pardon means accepting legal guilt. You can’t keep fighting a case saying you weren’t ever guilty.
For an example of how far pardons go look at Nixon. The case was still being built, and Ford (idiotically) deemed that proceeding with a trial of a former president over election misdeeds would do too much damage to the nation’s trust in its political system. Nixon didn’t stand trial. Nixon only pled guilty by acceptance of the pardon. But because of that, had he been able to run again (he’d hit his term limit) and tried, he would’ve had a court case over if his crimes prohibited him from running again, same as if he’d gone to prison for them.