Step one, confirm that you know it is a broken house rule.
In this particular case, its quite clear that the ruling is remarkably broken. For other cases though, examine how it might affect the balance (e.g. do similar effects cost more to pull off). "Why doesn't everyone do this?" is an excellent question to ask.
Step two, determine if you are OK with this.
You have also established you're not OK with the ruling, but it is worth asking if you'd rather not rock the boat on this matter. Consider both yourself and others (it may be that someone else at the table also hates the ruling). If everyone is having fun at the table, then why bother?
Step three (A), talk privately with the player for whom this house rule was first introduced.
Usually I would advise talk to the GM first, but in a case like this, where there is a player who suggested the rule, I think you should talk to them. After all, if they stopped using this rule, it would seem likely that the whole matter would stop.
Absolutely have this conversation in private/offline from the game.
When talking to them, I would advise the following steps:
(Honestly) speak of your enjoyment of the game as a whole. Hopefully on some level you do enjoy playing the game, and playing it with them. This should be an effort to help maximize the enjoyment of the game for both of you.
State how the recent change with the house rule has negatively impacted your enjoyment. Again, "play nice" would be my advice here. Don't let it get heated, but at least say that sitting back while you watch them summon puppies inside the boss, thus killing them instantly, isn't all that fun for you.
Now the tricky part, lay out your argument against the house rule. Show why its broken, why the ability isn't supposed to function like that, and why in allowing that, it is stepping on the toes of everyone else. While it might appear to be fun in the narrative of it all (and sure, it is funny, at least the first time), its not a good thing to base a game around.
If they're open to stopping, ask if they'll talk to the GM with you. If they're not open to stopping, consider if you're willing to escalate this to the GM, and let them know.
Step three (B), talk privately with your GM
This is about the same as three (A), only with the GM, with similar advice. State that you enjoy the game. State that the ruling is hindering your enjoyment. State that the ruling causes more problems that its alleviating. If the GM won't back down, inform them you'll be bringing this up with the group for their opinion.
Step four, speak to the group as a whole
This is kind of your last option with regard to fixing this. At this point you should bring up your grievance to the group as a whole, either before or after a session. Again, state how much you enjoy the game, and how this change is making you (and hopefully others) feel less useful, or less challenged. Lay out your argument that this is a fairly broken rule, and that without other significant changes to the game (ones your group is certainly not prepared to figure out). Hopefully other players will agree with you, but do try to play mediator as well. Don't let your dislike of the house rule turn this into a full argument.
Step five, determine how you feel about continuing in this game.
If you've gotten to this point and have still been unsuccessful, you'll have to decide if you want to keep going in this game. If this house rule is such a detraction from your enjoyment, perhaps you should leave the table. If these other players are your close friends and core gaming group (hopefully one does not find themselves in this situation), then perhaps bow out until a GM change or a new campaign.
Remember, your goal ought to be to help make the game as enjoyable for everyone at the table.
- Don't show them this topic and use it as ammo for why their idea is bad.
- Don't try to abuse this rule to prove how bad it is.
- Don't make it so much about the rules, as it is about enjoyment of the game. If they're using this ability to negate the need for anything else, that is taking much of the joy of the game from other players.
- If you're at the table, remain a good player. Try to not mope, be helpful.
- If you're at the table, observe rule 0. Beyond voicing a basic objection to a questionable ruling, don't disrupt the flow of play.