So my GF and I want to do Recruit A Friend (RAF) so she can grant her Monk as many levels as possible when MoP launches. For that purpose she invited me to the RAF and I created a new account. If I now connect this new account to my already existing old account, will RAF still work or does that defeat the purpose of RAF and makes us unable to profit from RAF anymore?
You can merge a WoW account that has not been converted into a Battle.net Account, but not two Battle.net accounts.
I was able to do this back when account merge and RAF was fairly new. You can recruit myself and immediately added a new WoW license to your Battle.net account (and dual-box if you wanted to).
According to this MVP post, As long as you have they are on two separate accounts, you should not lose your RAF links/benefits, unless you transfer the characters of the linked account.
If you want to merge two Battle.net accounts, you'll have to contact the Accounts and Payment department.