There’s no difference. Both are trespassing and should be treated accordingly if the owners are so inclined.
But there is a difference. At the abortion clinic two people enter and only one exits.
(1) The atheist in slumber1's example is specified to be "handing out literature" and not "trying to protect someone who is about to be beheaded and dismembered."
You're right in thinking that handing out literature is not an absolute right (not always and everywhere) but attempting to save someone about to kill or be killed is not just always and everywhere a right, but a duty.
(2) Even if the arrestee was indeed just handing out literature (without any larger justification of preventing imminent bloodshed), a penalty of 88 days plus 92 days (total 6 months in jail) would be excessive.
The excessive severity of the penalty was apparently motivated by the judge's view that Mary Wagner's actions were "aggressive" and they "victimized people," when what she actually did (according to the record) was open a door, give one or more women roses, and speak to them by offering to help them.
Not aggressive, no victims.
See the differences?