This is, of course, your choice as a DM. It always is. But if you're looking for justification by the rules, the spirit companion seems to be balanced. While attacks on it always hit, they have to pass the damage threshold and, yes, at low levels it will be very hard. At higher levels, I can see it passing the threshold and hitting the shaman for a lot of damage, but think of it more as you, the shaman, being up in combat and getting hit as if you were a melee combatant. Clerics and warlords suffer from this as well and while their defenses get more of a boost than a shaman does, the shaman also can rely on tanks to pull the aggro off of mobs and grant combat advantage to rogues, in addition to doing all of it's other powers. The drawback, in my opinion, isn't enough that you need to off set the damage threshold and it honestly could make it much more powerful.
Think of it like this. While the spirit companion will deal a healing surge worth of damage to the shaman when it goes away, that might be 20 points of HP for the shaman, the attack might have been upwards of 25+, making the hit on the companion less of a good option for the one doing the damage. If I was a smart monster, I might start to see the advantage of going after the shaman instead of the spirit companion, since I can proc status effects, on-going damage, ect. On a spirit companion, I might waste an encounter or recharge on it and only do a nominal amount of damage to the shaman, who's going to summon that beast up next turn again.
Opting for keeping it the way it is, but again, if you are the DM and it's your game, the ball is in your court to rule on what a good number would be. I would assume a good number to be is healing surge value. It will start much smaller for low levels, but it will increase every level with the shaman's HP. However, this can potentially be very high, as you're looking at around 40+ for final epic threshold as apposed to 25 for the normal one.