Those players that are currently linked via the Recruit-A-Friend system can rest easy -- although the ability to sign up for the program is temporarily unavailable, players that are currently using the program will be unaffected, and any rewards that have not been claimed will still be available when Recruit-A-Friend goes live again. As an additional note, the official announcement suggested that players participating in the upcoming program will have more rewards available to them.
The exact details on this tantalizing bit of information have yet to be released, but this is likely referencing the points made in the patch 5.4 Developer Round Table released last week. Along with multiple rewards, the new system will be accessible via in game interface, and reward a token instead of a mount. The token can then be redeemed for a variety of different rewards, and those reward might possibly include retired Recruit-A-Friend mounts as well, although that hasn't yet been confirmed. For now, we'll have to wait and see what the new system entails, and exactly when implementation will take place.