Imagine a scenario if/when btc breaks 10000$. This would square up 1 mBTC to 1 USD.
1 mBTC is 0.001 BTC, so it would be worth $10. 1 mBTC was worth $1 when the BTC price was $1,000.
Ultimately, it's impossible to solve this without convincing the people who create clients. You would have to encourage wallet developers to alter the units, one way or another.
If they did that though, they would have to very clearly clarify that they're talking about mBTC or bits rather than BTC, and that could be annoying.