Sorry but Gintoki was a pretty chill guy even during the war, he wouldn't randomly kill any amanto like that, only inside the battlefield. First, you should think in what time are you setting him, pre-Utsuro, post-Utsuro, after the ending. If you make it pre-Utsuro, you could make war Gintoki try to find Takasugi wondering why he is trying to destroy the country, after all I'm pretty sure no one of the joui four would have the courage to tell him what happened when they lost, so finding the truth could be challenging. Shinpachi and Kagura are cluess at this point of time, so they would be curious as well.
I suggest to watch some gintama movies before writing if you didn't, they should give you some inspiration like 'Gintama the Movie: Final Chapter – Be Forever Yorozuya'
I wouldn't trust that movie very much since has been made before the Utsuro reveal, now it filled with plot hole, like why Utsuro would wait 5 years to destroy the planet? What Takasugi was doing in the meanwhile? Since the Altana on Earth is special I doubt the Tendoshu would easily let the planet to become a distopya. Also I bet Utsuro would mercy kill infected Gintoki even only to be auto-ironic.
For inspiration and to get ideas, not to use it as is, for example, he can make a parallel world and make changes to Utsuru's story and Takasugi's, as in, perhaps in that world, the fight never ended meaning Gintoki never founded the yorozuya for example and is still living as Shiroyasha because the war is still on and maybe progressed to a whole new level... you know, it is a fanfiction, fanfictions don't necessarily need to follow the same plot as the original
the idea you are saying doesn't have anything to do with that movie though LOL and when I said the Fanfiction had to follow canon? even if doesn't follow canon should still avoid plot holes. It's just that the war for them started because Shoyo sensei and in that movie isn't even mentioned and there isn't much about the war at all apart some cool fighting scenes so I don't think is a good idea to use it as reference, apart that I'm sorry to have misunderstood the post