彼女は役に立つと私は思ったのだが、実際はいない方がよかったのだ。

、。

I thought she would be useful, but actually it was better without her.

Literal

She [topic-は] useful [quotative-と] I thought [was-のだが], actually not-being better [was-のだ].

~のだが ('the thing was...but') sets up a disappointed expectation. 実際は ('in reality') introduces the contrasting truth. いない方がよかった ('it was better for her not to be there') uses 方がいい for preference.