that is expected behavior because deployments in workbench are independent meaning runtime engine does not keep any relationship between them even though it would keep it there is no enough details about what shall be disabled and what not. So engine could not take the decision about disabling start timers as in some case it is desired on others it's not.
So simple solution (though not always possible) is to undeploy old version while deploying new one.
If that is not possible separating processes into different projects might be the way to go. That means you can include processes with start timer events into another project then other processes that change more frequently.