Yes, thrush can make them lame, esp in the heels. But generally it's more the things that go with - & often cause - the thrush that are the real issues. Eg contraction, weak, inefficient frogs / digital cushions. Interesting that he has more contraction in one foot than the other. Yes, easyboots or such will help support him & should make him comfortable & able to exercise while he's healing. If his heels are a little high, frogs a little receded & contracted, frog support pads inside the boots would probably be a good idea too.
BTW, going the boot/pad route, take a look at all the Easycare 'comfort pads' & the likes, then go to your shop that sells foam rubber & buy some similar & cut out appropriate size/shapes - should save you some $$