Gotta have some way to waste peoples IP right? Riot wants your money.
I wouldn't get rid of them though, just remove their IP cost completely (and give refunds!!!), and lose the cost of extra rune pages. Runes are a nice way to give a little customization to your champion.
You don't have to get rid of lower tier runes either, see it as playing with a handicap. And if we could actually customize the bots lower tier runes would be nice for newer players to give to the bots to slowly work up to the higher tier runes other players use.
Its the same shit with unlocking champions, the IP costs are absurd, get rid of RP being able to unlock champs and get a pricing scheme basted on how difficult a champ is to play, keep the prices reasonable and leave the RP bullshit for skins.