What I think happened is they were both very drunk and emotional because of this Jacqui was too out of it to signal she didn't want sex and froze in fear and Gilly was too out of it to read any signals. Really sad for both of them.
It's a good storyline though different to the usual plot of a random bad guy turns up and rapes the woman kicking and screaming. I'm glad they used two well known, well loved characters and raised all these question. Jacqui certainly felt like she was raped and Gilly was the perpetrator so does that automatically make him a rapist? What if his intentions weren't malicious and he genuinely didn't realise she was saying no? Then you got Rhys in the middle who is Jacqui's husband but has also been Gilly's best friend since they were little.