Good question - I ran into this issue when I got Lydia during my first play-through. She would charge in and kill everybody so no progression on armor and weapon skills there. Of course, you can improve your archery...
I think you have a couple good alternative:
* Only use followers strategically (have them wait outside a ruin and use them as a mule for loot)
* Get good at conjuring so you can summon atronachs as needed (very, very fun in my opinion)
Good luck!