I think that removing bonding would really hurt the non-PvP taming population. The damage and speed are the reason people want the pets in the first place, and those are respectfully balanced. A dragon should be hard, and a nightmare isn't called a Nightmare because 2 great harts can own it. The stat loss is just another method of time consumption, something this shard seems to avoid with fast skill gains, etc., and wouldn't really change anything except make tamers bitch more. That being said, I feel that removing the ability to recall with bonded pets would be the best solution. First, it's the speed factor and the element of surprise of recall that give it an undue advantage. "Wow, it's nice and peaceful...*poof*, white wyrm on your ass and a nightmare to follow. It also works in the reverse, a fearful and outnumbered tamer sees a group of enemies approaching, *poof* huge dragon and tamer gone. Gate would cause the tamer to use strategy in timing, and rune locations. Like back in the day when the troops would flood in on horseback, the battle would rage, and the tamers would come in a few seconds later from a different location and then the war would really begin.
Being forced to use gates is not that much of a disadvantage, but I think it would be just enough. The blue population would not be too upset with the loss of recalling with bonded pets, it's just an ash instead of a moss and a bit more mana. The extra mana used in gate would also make the tamer less of an instant threat in PvP, when gating he couldn't do a full dump after casting a 7th Circle spell.
Since the problems with tamers seem to be centered around their use in PvP, I think this addition would add neccessary disadvantages to the PvP system while not inhibiting the non PvP action too severely.