It should only fire if the email changes. Since you're using reconfirm email it basically should never fire for a profile edit update, but only after they've confirmed the change. Your action probably should be configured as follows.
Global
Triggers: onAfterUserUpdate
Type: Usergroups
User: Automatic
Access: Everybody
Conditions
1: [var1_email] Not Equal To [var3_email]
If that condition isn't working right you can try the below instead.
Code:
[email] Not Equal To [var3_email]
You can add your other conditions after you're sure it's working for your usage. You may or may not need to use Reload User. Sorry, I've never used the usage you're trying nor is the above tested. Adjust as needed. Note you can access URL variables with [get_VARIABLE] so worst case you check that the action is being fired on the confirm email page using its URL variables.