From our POV, there is no defense of totem-stomping macros.
If you want to take the time to give your pet a command and a target to kill a totem, great. But to be able to neutralize a core mechanic of the class so easily because you are clever enough to copy a macro off of the Internet is not skill.
The only reason they still exist are technical limitations, not because we like the design. (And please don't feel the need to offer your technical suggestions. :) )
The OP argues that easily killing totems with almost no effort due to macroed pet commands is just balance, it's the counter to totems. This argument isn't too bad, except that it fails to distinguish between "counter" and "trivialize." A macroed pet could potentially kill totems as fast as they are created and suffer only a small DPS loss from the pet being busy.
But perhaps this isn't all that different from an enhancement shaman purging buffs. Or maybe it is. The two other specs of shamans would suffer DPS or healing losses from purging, due to being unable to cast. In addition, there are many dispel resist talents or even some talents which reactively punish dispel, such as unstable affliction or life bloom. In contrast totems have no defense against one-shotting by a pet.
Are there solutions? Totem stomper macros could be disabled by blocking anything at all like the names of totems form macros. But that would hurt shamans as well. References to attacking totems could be banned, but that would be very complex and probably end up just being the first solution.
The simplest is just to buff totems: give them enough health to survive a hit or two. Maybe give them 10% of the shaman's health. That would give them 1.5-2k health, or something, I have no clue how much health a PvP shaman has. The number can be adjusted, but the idea is that a wand or pet cannot one-shot the totem but a melee attack or a spell will have no difficulty at all. This makes totems easy to kill, but not free to kill. That seems balanced to me.