How can I stop myself from picking up certain items for a Pokestop?
No, there isn't a way to avoid picking up certain items. However, you can delete items from your inventory. When you are viewing items, tap on the trash bin for the item that you'd like to reduce the quantity of. You'll then see a pop-up asking how many items you'd like to discard. Select the appropriate amount you'd like to get rid of and tap yes.
There is not, you will collect the items whether or not you tap on them. However you can simply trash them in the items menu. It will ask you how many you want to trash and that will free up your inventory!