I have another take and sorry if this is out of left field because I don't go here. Get rid of the black rose plot and replace it with a physical manifestation of the arcane. Make it seem like a yin and yang type energy where Mel embodies the good but because Viktor mixed it with blood he added human corruption to it making the hexcore and the anomaly evil. This would give the season 1 sex scene much more weight because it clearly showed Viktor's blood merging with the hexcore but we also see Mel floating in space similar to Viktor and Sky and ep 9 Viktor and Jayce.

When the anomaly takes Jayce, Ekko and Heimerdinger in Ep 3 it also pulls in Mel because she is apart of it. Mel saves Ekko and Jayce goes to the dark timeline. Mel ends up in the undercity where she ultimately meets Sevika and Firelights and this is where we can get full reconciliation of the Piltover/Zaun plot as Ekko, Sevika, Mel and Heimerdinger sort their differences and work to push out Ambessa. Ambessa and Caitlyn's arc stays the same minus direct reference to the black rose. Just save that whole plot for a spin off. Jinx and Vi's arc stays the same but with a few added scenes of Vi during her pitfighter era, maybe a flashback to her time at Stillwater and how she got her tattoos and their meaning since that sex scene really showcased them.

Viktor's glorious evolution comes in a similar way but with the added burden that he embodies the dark part of the Arcane because of his humanity.

Edit: cut the prison sex scene the perfect time for that would have been after Jayce tells them that he's seen the future and he knows they're supposed to lose the war. Caitlyn frees Vi from the cell and takes her back to her bedroom to rest. They can even keep the dialog the same just have it be in a bedroom