The solution to the automatic activation issue people are complaining about is simple. Add a hook that allows you to disable auto activation. If you have done this then installing would not auto activate. If you have not then it will behave as intended.

People need to remember that Developers != Average Users and Average Users > Developers. WordPress needs to take these steps to make WordPress more friendly and improve the overall UX for AVERAGE USERS. Developers will need to learn to deal with that fact.

So instead of complaining about features like this, suggest alternative solutions that will address this concern. I've already done so above. Problem solved.