It's a bit much to believe that nuns in the 1960s were spreading liberalism, cake and gay acceptance around the east end of London.
Yes - the storyline with the gay bloke was ridiculous. Even today a lot of people would be rightly appalled at a man cheating on his wife and using public toilets to have sex in. Men thinking their sexual kicks are more important than basic consideration for others doesn't really provoke sympathy from me! In contrast, Patsy and Delias' storyline actually highlights the important issues involved and makes you feel sympathetic to them.
There seems to be a lot more out of place stuff on CTM as it continues, stuff that's wrong for the time, and really over the top storylines. Eg. the au pair situation is being laid on a bit thick. I think the Turner's house must be on ley lines, so every event or emotion is cheesily amplified! 
And when Valerie was talking to Lucille, it just didn't sound right for the time period. I could believe the nurses/nuns would be sympathetic to her, maybe say something firm to anyone making negative comments, but saying "What that woman said was unforgivable" just sounded like a modern person speaking. These nurses would have witnessed all kinds of human unpleasantness and I don't think racism would have been treated as worse than any other thing.
Also Sgt. Jobsworth saying, in classic pantomime policeman style "Well, well, well..."! But I kind of love him anyway.
I reckon he might deliver a baby or something later in the series.
And completely random, but it annoyed me that the Turners were all fully dressed but the baby was in a little summery outfit to signify "it's warmed up". (In fact the mismatch of clothes in this way generally annoys me on TV!)
I do like CTM, honest!