Fortunately, you can tell Gmail to really mute such threads — until a message in the conversation is address to you and only you. (Somebody specifically adding you as a To: or Cc: recipient will also bring the conversation to your attention.)
Mute Reply-All Threads Successfully in Gmail
To have Gmail hide new messages in muted threads unless they are address only to you or somebody specifically adds you to the conversation:
- You need not do anything in Gmail's current (as of June 2013) version. Muted conversations will pop back into your inbox when a message in it is addressed to you (and only you).
(Updated June 2013)