Nechama Leibowitz, in this letter, outlines her approach to this question. I think a basic level of intellectual honesty demands that if someone says a good pshat, that we use it. If they got it right, they got it right. To the sources regarding kisvei hakodesh written by an apikores, I think one must distinguish between the ideas and the physical books. The alternative is nonsensical. I'm supposed to ignore what I think is a correct idea simply because of who said it?
Furthermore, on a practical level, I don't think the label of apikores can be so simply applied to all the "non-frum" sources. If someone did not grow up frum, its arguable their status is a tinok she'nishba, not an apikores. Additionally, it's debatable exactly what constitutes apikorsus. One man's Rebbe is another man's apikores. There's a lot of rishonim who did not conform to all 13 of Rambam's Ikkarim, yet they are accepted halachic authorities. The question of who and what is considered out of religious tradition is a much more complicated sugya than how it is presented in other answers to this question.