The halachah regarding sefarim is an extension of a law in the Talmud about a sefer Torah. Both relations and a sefer Torah (and, by extension, sefarim) are considered holy. But there are different types of holiness, and each is holy in its own way.

Holiness during relations is of the type which seeks to elevate our most physical activities, so that even when engaged in them, we are not purely animal. Sexual relations can be more holy than other such activities because we have an emotional and spiritual connection to our spouses, because our sexual pleasure is heightened when we give pleasure, because the act is reciprocal. When a couple is attempting to conceive, there is also the holiness of human creative endeavor, of turning our drives towards a form of emulating God.

Marital intimacy is holy in its sphere. Its holy aspects do not transform it into an act that should be performed in every setting.

Neither is the holiness of relations diminished by keeping relations separate from the holiness of the Torah scroll. This is but one of many halachot and customs reflecting the obligation to show respect to the Torah. For example, we don't sit on the same surface on which a sefer Torah also rests and we stand when a Torah is lifted, even though there is nothing inherently objectionable about sitting.

We hope this helps your kallah. Please feel free to get back to us with any further questions.