A few ways you could handle it:
- Each and every spell has a rider effect that kicks in if still memorized, either baneful or boonful. The downside to this is that you must individually balance each spell. It also gets to be a lot to keep track of at higher levels.
- As above, but cap the number of active effects. This has fewer but still significant issues.
- Introduce "reserve feats" a la 3.5. Basically, in 3.5, you could take feats that said things like, "Throw a mini-fireball, affects one creature, deals 1d6 damage per spell level of the highest Fire spell you have memorized." You could come up with a list of 7+/-2 Reserve Feats then let players select them. I would either allow a number of feats equal to MU Weapon Profs (so 1 at level 1, then another at level 7), or perhaps a number based on INT score + extra ones with weapon profs (to create growth with level). I'd also consider allowing players to "retrain" their Reserve feat every level up.