I've started watching this again, and it's just as unsettling as I remember. In fact I'm amazed I sat through it as a kid, scaredy-cat that I was.
It's interesting that they didn't feel the need to bung in a load of supposedly creepy incidental music, or any incidental music. The best TV shows seem to share this trait.
The only way to get decent scifi back then was to sell as kids/family tv. And that's before you mention the scarier Dr Who episodes.
When you look back on it, there are loads of kids scifi/fantasy/drama tv shows that were quite spooky and very watchable (and rewatchable today). Children of the Stones, Into The Labyrinth, King of the Castle, Chocky etc etc.
Sapphire & Steel was definitely more 'adult' and some of the things going on were very unnerving for a family tv slot. I reckon that most kids who watched it back then can remember the haunted train station, or the people with no faces. And apart from the episode with the children in it, there were few happy endings (the train station being one of the most chilling). Sapphire & Steel were not particularly benevolent beings. If someone had to suffer for 'time' to be adjusted , then it was a sacrifice they were prepared to make.
And I agree about the incidental music. There is a time and place for it (eg Jaws) but it has to be relevant to the show, and if you can do it without the incidental music having to tell us 'this is a scary bit' then when the fright happens, it's far more effective.
I feel the same about comedies with laughter tracks. If the show has to tell us when to laugh/what is funny, then it obviously isn't doing its job. And whoever thought up having a laughter track on MASH - I find it unwatchable with the canned laughter turned on.