so was Homelander actually telling the truth?

Probably. The video of her exiting was ambiguous and we only have Homelander's version. Season 2 we will presumably get the former Mrs. Butcher. But again, I say probably. The look she gave Butcher seemed to be "damn, what is HE doing here, this is bad..."

Homelander has the least incentive to lie, there are zero consequences for him either way.

This whole thing was quite different and a lot darker in the comics. She never said anything about the rape and the first time Butcher got the whiff of it was when the superbaby burst from her tummy and started burning shit with his eyes.
Took an effort to put him down. She was dead, obviously.
They clearly decided to go into a different direction in the series and make the supes somewhat fragile under the surface. In the comics the reader has zero sympathy for 95-97% percent of the superhero characters.

I think it was/is ambiguous. She seemed flattered, and being with a super hero would be overwhelming. Obviously, Homelander has huge psychological problems. I think what a lot of people are missing is that Homelander didn't really think about her at all. She was a one night stand if that. He didn't wonder much about her after she disappeared.

The meeting between Homelander and the Doctor was key. The doctor recognized that raising Homelander as he did turned homelander into a psychopath. "It was my greatest mistake." So the Doctor and Stillwell hid the pregnancy, and of course the mother never told the boy who his father was. They didn't want Homelander anywhere near the child because of his psychological problems. I assume she was afraid of Homelander as anyone else who knows him very well.