There is an option to use connections (instead of bribing) to avert an expedition, if you have at least 25 rep with them. I never tried it (since I did not have the rep at the time).
I think what he's getting at is that (as has been mentioned previously) it makes little sense that expeditions the size of full-scale war fleets would be sent at an ally with 80+ reputation in the first place the same as if you were at neutral reputation or even hostile. Yes you can use reputation to avert them, but it seems very jarring - especially with the frequency they can be sent.
As has been mentioned in other threads, I think the main issues are:
1) AI factions have such crappy colonies - and the player can easily build such ridiculous money-factory colonies - that it's easy to out-produce every major faction fairly quickly and draw their ire
2) Expeditions, even though they're supposedly "deniable", are in essence full-scale war fleets with the best tech available to the sending faction
3) AI factions apparently have endless supplies of ships, supplies, fuel, and men beyond what their colonies could reasonably produce to send so many expeditions. And smashing them utterly seems to not make any difference
4) Reputation has no impact on frequency of expeditions, size, amount of warning, or diplomatic costs/options. Once you start establishing colonies, it essentially becomes a resource that the player needs to constantly keep up with every faction to avert expeditions or else simply endure and crush the inevitable waves of expeditions. There are so many ways to gain faction reputation, and the player only has so much time. Hopefully the "Orders" tab will also eventually allow friendly fleets to be sent on rep-raising missions.