aefimov - The JIRA integration plugin is a bundled plugin and we don't expect people to run without it. We don't test Bitbucket Server without the plugin. If we fix the branch creation page so it works without the JIRA integration plugin, it may break again with the next release. As a result, I doubt we'll ever work to make the branch creation dialog work without the JIRA integration plugin.
It's much more likely that we'd fix whatever problems you're having with the JIRA integration plugin so you don't need your own plugin (or - at least - can run Bitbucket Server without disabling the JIRA integration plugin). Can you give me some specific examples where it's detecting JIRA issue keys in strings? What specific problems does that create for you and your team?
If Bitbucket Server - JIRA Intergation is enabled, then all JIRA keys are drawn as clickable, even if not JIRA Application Links is configured. This is clashed with our tracker integration.