Separate version control from deployment. I don’t feel sure I understand the problem from your description: what does “a lot of the scripts need to be deployed at different times” mean, and what does that have to do with branching?
The scripts might involve a change to how a user is added to the system and another might be a change for how a user is updated. The "update user" script cannot be deployed until the "add user" script is deployed.
Your version control and deployment processes should move your applications from one working state to another working state. Temporal runtime dependencies such as "A must run before B" should get handled at run time, either by making A execute B when it successfully finishes, or writing a higher-level script that runs them in order only if both exist.