The Beatles' Anthology book published in 2000 quite neatly lists the opinions of each of the Beatles about Manson's appropriation of 'Helter Skelter'. Firstly, to the English in the 1960s, a Helter Skelter was a specific kind of amusement park slide (e.g., one that was spiralling), and the lyrics describe exactly that:

When I get to the bottom I go back to the top of the slide

Where I stop and I turn and I go for a ride

Till I get to the bottom and I see you again

In a 1980 interview Lennon called it 'Paul's song about an English fairground'. McCartney, in the Anthology says that in writing the song, he was aiming to just get loud (after having read Pete Townshend interviewed in Melody Maker saying The Who had just made the raunchiest, loudest, most ridiculous record ever):

That was really all I wanted to do - to make a very loud, raunchy rock'n'roll record with The Beatles. And I think it's a pretty good one."

McCartney, as quoted in the 2000 Anthology book, describes his understanding of what Manson was about, and his reaction to the events:

Then it got over to America - the land of interpretative people...Charles Manson interpreted that 'Helter Skelter' was something to do with the four horsemen of the apocalypse. I still don't know what all that stuff is, it's from the Bible, 'Revelations' - I haven't read it so I wouldn't know. But he interpreted the whole thing - that we were the four horsemen, 'Helter Skelter' the song - and arrived at having to go out and kill everyone.

It was terrible. You can't associate yourself with a thing like that. Some guy in the States had done it - but I've no idea why. It was frightening, because you don't write songs for those reasons...it all went wrong at that point but it was nothing to do with us. What can you do?

The Anthology book, of course, is an authorised book from 2000, twenty years after John Lennon had passed away, murdered by a similarly ...interpretative American, and so we should be a little wary of the Beatles' reactions as portrayed in the Anthology. Interestingly, in order to get John's views on Manson, they quote a 1970 interview and a 1980 interview from Lennon, the 1970 interview in particular giving a more contemporaneous reaction to events. In 1970 Lennon said:

[Manson]'s barmy, he's like any other Beatle fan who reads mysticism into it. I mean, we used to have a laugh putting this, that or the other in, in a light-hearted way. Some intellectual would read us, some symbolic youth generation wants it, but we also took seriously some parts of the role. But I don't know, what's 'Helter Skelter' got to do with knifing somebody?

In 1980 Lennon pointed out - probably a bit too defensively - that the two songs Manson was most fixated on ('Helter Skelter' and 'Piggies') were written by Paul and George respectively:

It's got nothing to do with anything, and least of all to do with me.

Ringo in the Anthology doesn't focus on being responsible for the songs at all, but instead on how 'everyone' [in the counterculture] was feeling at the time:

It was upsetting. I mean, I knew Roman Polanski and Sharon Tate and - God! - it was a rough time. It stopped everyone in their tracks because suddenly all this violence came out in the midst of all this love and peace and psychedelia.

George Harrison, in the Anthology, saw Manson as part of a wider appropriation of the Beatles to various peoples' own ends, implying that Manson would have found some other rationalisation for his actions if the Beatles hadn't existed:

Everybody was getting on the big Beatle bandwagon. The police and the promoters and the Lord Mayors - and murderers, too. The Beatles were topical and they were the manin thing that was written about in the world, so everybody attached themselves to us, whether it was our fault or not. It was upsetting to be associated with something as sleazy as Charles Manson.

Another thing I found offensive was that Manson suddenly portrayed the long hair, beard and moustache kind of image, as well as that of a murderer. Up until then, the long hair and the beard were more to do with not having your hair cut and not having a shave - a case of just being a scruff or something.

Overall, the Beatles seem to have seen Manson as a particularly unpleasant part of the hoopla that had been surrounding them for 5-6 years at that point, that they couldn't really predict or control, and they were upset that their music had been attached against their will to some particularly unpleasant events.

Finally, in a 2018 interview with the NME, McCartney said that the whole thing put him off playing the song live:

Well, that put me off doing it forever. I thought, I’m not doing [‘Helter Skelter’], you know, because it was too close to that event, and immediately it would have seemed like I was, either I didn’t care about all the carnage that had gone on or whatever, so I kept away from it for a long time.

But then in the end I thought, you know, that’d be good on stage, that’d be a nice one to do, so we brought it out of the bag and tried it and it works. It’s a good one to rock with, you know.

According to setlist.fm (which is probably reasonably accurate), McCartney first played Helter Skelter with his live band in 2004, a good 35 years after it was first released, and has played it hundreds of times since.