For what it's worth, I think that's a good call. If I was using Arcane Thesis I'd tend to rule it to only allow a total -1 reduction to the spell level, not -1 per metamagic feat, but your way is fine too.
I briefly played with Arcane Thesis in a PbP game, because the GM had specifically asked us to make powerful characters. I didn't even pick a particularly nasty Thesis spell (Rainbow Beam - Split + Empowered for 15d12 damage as a L4 spell, or add Ocular Spell for 30d12 in a full-round action at the cost of two L5 slots), and it still broke the first few encounters (after which the game collapsed).
Arcane Thesis, applied to a direct damage spell, can raise an arcanist's damage output far above what you would normally expect. The really nasty options aren't ordinary damage though - consider spells that do no-save ability damage or negative levels. A L13 wizard with Arcane Thesis (Enervation) and three metamagic feats can lay down (4d4)*1.5 (average 15) negative levels as a full-round action. If you decide to allow Ray of Stupidity (which I would recommend against, independent of Arcane Thesis), one full-round action and two L5 spell slots can get you an average of 20 points of Int damage - although really, you'll probably just want to stick with the L4 standard-action version: average 10 Int damage frequently suffices to incapacitate either big dumb foes or enemy wizards.
Oh, and just a minor pet peeve: Ray of Enfeeblement imposes an ability penalty, it doesn't do ability damage. This means it doesn't stack with itself. Empowering Ray of Enfeeblement works to increase the penalty, but if you split or twin it for extra rays, you take the largest penalty from an individual ray, you don't add them all together.