I think your worrying a not much. There are ways you can prevent things from entering your lines..... Plus you have the backup line in place. I would drill the primary bulkhead bigger than the backup. JMHO!!!
As far as putting a valve on the drain line, I think we are over complicating things. This method is done all the time will no bad affects. Again there is a backup in place, an theoretically your not restricting the drain line; you are merely altering the flow pattern. That is why I suggest with you concern to drill bigger than 1". Worse case scenario why couldn't you drill 2 drains and a backup?? You could leave 1 line straight to the sump, the other to the sump and "valve it", and the 3rd as your backup???!