I think I'd be doing that like this. I explain my reasoning. Take it or leave it.
The emotitoy rolls using its rating. If it gets net hits in an opposed Sense Motive vs. the target, then it can relay its findings to the runner. If it doesn't, it would still relate what it thought it found to the runner. This in itself could be funny as hell.
So at best, it's guiding the runner's actions, not supplying dice to the runner. I get that because of the following wordings:
QUOTE (Arsenal @ p. 60, Empathy Software)
Empathy soft ware can be discreetly used in real time during negotiations or social interactions, adding its rating as a dice pool bonus to the character's Social skill tests.
In that entry, the implication is that it's installed in a sensor that the
runner is using (in your goggles/contacts/etc.) and running "in" the runners consciousness. The support for that notion is found in the emotitoy entry as illustrated next.
Emotitoys have their own sensor package, as in their description
QUOTE (Arsenal @ p.57, Emotitoys)
Shadowrunners have also embraced the emotitoy craze, bringing their "friends" along to meets to get an edge during negotiations, using the toy's sensors and empathy soft ware to get a read on the other side.
Emphasis mine.Also, keep in mind exactly what it's possible to glean using the Empathy software:
QUOTE (SR4A @ p.139, Judge Intentions)
A character who wants to use her natural empathy to gauge another character's emotional state, intentions, or honesty can make an Opposed Intuition + Charisma Test against the target's Willpower + Charisma. Note that this sort of "psychological" evaluation is never a certainty--it's just a way for a player to judge what her character "feels" about someone else. It should never serve as a lie detector or detailed
psychological analysis. The gamemaster should simply use it as a way to convey gut feelings the character gets when dealing with another.
So at best, it's like having a very, very limited ability face that can give you advice. One that can tell you that it thought that the Johnson seemed a little angry when he answered your last question (and if it got some hits, it might even be right

).
I don't see at all how that encroaches on a Social Adepts potentially ludicrous ability to walk all over anyone else in social interaction. (And I'm not saying that as a harp on social adepts, they're cool.)
edit to add:
I can see that this wouldn't really mitigate your issue with the Empathy software itself, Larme, but remember that these games aren't played in a vacuum. If your group's face wants to be the guy that's really good at social stuff, then the other players shouldn't be loading up massively good Empathy software on high rating sensor suites. But for a group in which nobody really wants to play a dedicated face, this is a neat way to have somebody that's capable of a few social tests without the GM having to dumb down every Johnson or fixer so as not to drastically outgun the players in negotiations and stuff.