With your houserule, re-rolling would happen much more often.
I'd like to talk about the statistics of rolling a little bit before talking about balance directly. On average, a Fate die gives +0, since there's an equal chance to get +, -, or 0. If you allow a player to only reroll some of their dice when invoking an aspect, then you effectively give them +1 for every - they rolled, on average, while also giving a chance to get +0 (by getting another -) or +2 (by getting a +).
Statistically speaking, this doesn't change the numbers very much. If there are 2 -s, then it's equally good to get a +2 as it is to reroll those -s. If there are 3 -s, then it's better to reroll either with your houserule or without it. However, since this houserule gives the players a fairly significant chance to increase their roll by +2 per - they reroll, I would expect players to do this much more often than they choose to reroll in normal Fate. It's been my experience in several different systems that if you give a player the ability to have a decent chance at turning a negative into a positive, they'll take it. Also, rolling dice is fun for many people, and this houserule makes it statistically valuable to reroll in many more circumstances.
I would expect that, for most players, the default use of an invoked aspect would be to reroll any roll with at least 2 -s, rather than getting the +2 directly. Players would only take the +2 if there was 1 or 0 -s in their roll, or if they generally felt unlucky and didn't want to chance another roll.