Things you can do that are within the rules:
a) Apply that -2 penalty to everything liberally.
b) Apparantly there is some errata in TaB that limits the spells abit.
Things you can do that are in the spirit of the rules, are implicit to the rules, and should be in the rules but not actually explicitly in them:
a) If the character adventures as a member of a different race (say the fighter is Polymorphed into a Stone Giant) apply the Stone Giants ECL when determining experience he will recieve from combat. This will do two things: His class levels will tend to go away, as he will not have enough XP to be leveled as a Stone Giant. Also it will tend to reduce experience sufficiently that being polymorphed is less tempting. There is some obvious reasoning to use should the character's complain: "But you are a Dwarf learning how to fight effectively as a Stone Giant. That doesn't help you as a Dwarf much, and a Stone Giant takes a long time to learn how to fight better than its already naturally bad self."
Of course this slightly bends the way the Polymorph Other spell is written, because the spell doesn't mention this. (It only doesn't mention this IMO because at the time PO was being play tested ECL was a distant thought in everyone's mind.) Losing class levels (but gaining ECL) in this way should elimenate (or reduce) the physical side effects of gaining levels only - e.i. Fort Saves, Reflex Saves, increased BAB, physical skills (balancing as a Stone Giant when you've practiced as a Dwarf is somewhat different), and Feats when they relate to physical activities (like Dodge and Whirlwind Attack for instance). It doesn't effect Mental skills like Will saves, mental skills (like knowledge), or spell use; although, you still must make the Will save or be at -2 on this skills as well.
The only drawbacks to this is that it requires a good deal of book keeping, but really no more so than when the character gains negative levels from a wight or spectre attack. Also, you will need some sort of rough estimation of the ECL of X sans its supernatural abilities (but that shouldn't be too hard and you need not be that precise). In play, I doubt this will come up alot once you implement the rule, because the reasons for polymorphing allies in combat will disappear.
Things you can do that aren't in the rules but should be:
a) Force a Fort save whenever Polymorph Other is used on a target (at the spell's normal DC) or that target permanently loses 1 CON.
b) Force a Will save whenever Polymorph Other is used on a target (at the spell's normal DC-4) or that target loses its mind and becomes permanently mentally an average member of the chosen form in motivation, alignment, intelligence, etc. This Will save must be repeated every 24 hours that the target remains in this form with the DC being reduced by 1 for each day that passes. Once the DC is low enough that the target can only fail by rolling a 1, he no longer has to save (e.i. rolling a 1 is not an automatic failure). The character is considered to be adventuring at his new ECL, and if the ECL of the new race is higher probably will have several less class levels (as above). Because the mind has changed, even mental skills (like spell casting) are not stable and may be reduced as above (and of course disappear altogether if the intelligence is too low to use spells). The new creature will resist changing its form back if it is intelligent enough to understand the intentions of the spell caster.
c) Limit Polymorph Self to 10 minutes per level.
