Commonalities:
1. Both have a cause for which they kill.
2. Both are (generally) not killing those in the same faction.
Differences:
3. You may be part of the same faction as the good, without taking an oath or even directly dealing with Fortress. Just by virtue of your own behaviour (of not harming other gold-auras). Becoming safe from Empire in this way is much harder, and requires either the Oath or special dispensation from Emperors and such.
4. Imperials may fight and undermine others in the same faction, e.g. inter-Sect conflicts or intra-Sect struggles for Elite or Leader status.
5. Related to 4, Imperials may also directly harm their subordinates without referring to higher tiers of oversight. Marans generally cannot punish a Squire without referring to the leadership or IMMs. The extreme is Anathema, whereupon the Anathema becomes #1 enemy. There is no such thing for Marans, except in the very rare case of a Maran becoming red-aura.