Stop him from following, to keep him safe from whatever is going on round the corner, and to let Yashiro have some independence to deal with something that has been bubbling away for close to two decades.
But shooting him was too much. Isn't there any other way to keep him safe??
I guess it also was self-sabotaging behaviour from Yashiro, a way to try and get Doumeki to reject him. Ultimately though, Doumeki would not willfully leave Yashiro, especially knowing he was going to Hirata, he says he would die for him, and has already nearly been shot in the head by Chestnut 2. Also, it's not like they are that far away, Yashiro is only round the corner of the warehouse, presumably he will be discovered at some point soon. It is what it is
OMG??????How can you shoot him? Why did you do that? Hm