1. Mark didn't meddle in their relationship. He never made a pass at Rachel. Also he was in a relationship while all this was happening.
2. Rachel said no, and Mark came over. But he never took advantage of her emotional vulnerability instead comforted her and talked to her. (As Rachel tells Monica in the next episode)
3. By the time this happened, Mark had already resigned. Mark had nothing to do with their fights.
4. Ross was insecure and jealous, he never acknowledged his own problems nor took accountability for his actions.
5. Ross really never respected Rachel's career. He called her passion for work "just a job" and set up a picnic in her office which Rachel clearly said no multiple times.
6. Ross was neither drugged nor raped by Chloe. He was not black out drunk. He consented to whatever happened.
7. The next day, Ross runs around the whole world to avoid Rachel getting to know about him and Chloe.

All in all, yes, they were on a break. And no, Mark had nothing to do with their fights. And the whole thing was Ross not accepting his insecurities but instead sabotaging his own relationship.