There are a few things that can be done to prevent this some easy others not so much.
First step would be making it a bannable ofense. That would decrease the ocurrence like it did for mudosa farm, some smartass players will still try though so rules must be enforced(like our friend feifei here probably still doing mudosa farm).
The next and hard step would be a complete rework to how guild challenge works. For starters , the first guild being the one to challenge isn't fair for anyone there which leads to alt guilds.
I came up with 2 possible solutions:
The first solution and my favourite would be increasing the amount of guild challenges a dojo has to defend on sunday, I would recommend 3 or 4 , don't allow the same guild to challenge again so we would have 3 to 4 different guilds challenges in the same day. For that though a 1 hour duration war is a bit too much, even for how it works currently. I would suggest decreasing time by half and doubling the points given during the war effectvely decreasing the time by half.
Let's talk rewards as well, defending a dojo should be fun and rewards are part of the fun for both sides. Guilds spend 1m to challenge and noone get's anything in return besides a budokai seed to one player. There is actually a rock that you get after the dojo ends ( which we didn't get one here btw) that could be repurposed to give the winner some reward in some npc.
the other solution would be changing the challenge from first served to an auction where the highest bidder will have the right to challenge the dojo, but then again the rewards should be compeling.