The dynamic between her and Oliver may have shifted, but Felicity has never been a moral compass for the Hood/Arrow/Green Arrow.
Arrow season 5 will continue in January 2017 on The CW.
The main thing fans can expect is for Felicity to formulate her own revenge plan for Prometheus.
Mericle suggests that any kind of conflict between and Felicity and Oliver will be downplayed, settled early on or else sidestepped altogether… although the last option is a longshot.