Yes, it is interfering with mundanes. I can't say where, but I have in mind that the rule is that magi can take part in crusades, so long as they are not using their magic (too obviously). I do not have a source on this and it might be just something from our games or it could be from a book...
That is a too broad generalisation, especially considering that the Order has a number of non Catholics (Theban Tribunal) and non Christians (hermetic sahirs in Andalusia). These are exactly the people who might bring a case of mundane interference.
Then this is self defence and evreything goes. This is their chance to throw sight+group damage spells willy-nilly. We had our covenant under siege from Baltic crusaders (Riga Sword Brothers, IRL real dickheads) in our game and it was great fun, as the "self defence" part let us use everything at full power for maximum destruction.
Now whatever happens, they can bring a hermetic case against the enemy wizard (assuming that they live long enough).
I wrote a siege scenario, but the players are expected to be on the besieging side.
What defending magi can do: keep repairing the rock, with Mu/Re Te the catapults will fire everything they can but the walls will be repaired within minutes, ie much faster than they can fire.
The magi can definitely use ReTe to grab the catapult shots mid air and return them to senders or to the catapult crew's friends.
Are the magi constrained to their Tower? because if they are, they are limited in what they can do, probably just throwing sight level spells at enemies who might arrive. Giving grogs night visions at night would be helpful (eyes of the cat) to keep guard. Can they do something for food/water? This might come into question if the siege goes down to a logistics stand off.
If they can fly/teleport out, then there is next to no limit to their mischief. Without knowing what the PC PC-magi have for spells, it is hard to give a full answer...