Well, it gives a boost to BAB that you wouldn't otherwise get, allowing things like earlier iterative attacks, a 5th iterative attack at 19th level (BAB 21 now), and earlier PrC entry. This won't break your game, but it will change it.
An easier way to mitigate the dip effect would be to only grant the +2 bonus per save once. So, a Fighter 1/Rogue 1 would still get +2 Fort and +2 Ref, but a Fighter 1/Barbarian 1 wouldn't get Fort +4. You'd only add the +2 bonus to Fort once.
Of course, this approach incentivizes certain types of multiclassing over others. Six of one, half a dozen of the other, I guess.