Wasn't 100% sure but a quick Google check states the new rep system won't affect those in parties or in your friends list. Its mainly targeted strictly towards playing online with random people.
Quote:
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Players who prefer to stick with a party of known people in their friends lists won't be affected by the reputation system changes, Lavin said. Those playing with random, anonymous strangers, though, will quickly find that they are matched up with people who have similar reputation scores.
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http://arstechnica.com/gaming/2013/0...tation-system/
I'd assume once you drop someone from a party or friends list, then they'd become affected until you bring them back.