My understanding is that they were, indeed, lovers, but that it was an experimental/hormonal thing (much like girls at a girl school may play around a bit with other girls because that's all that is available while they are going through horny adolescence). After all, novices and Accepted aren't allowed around men at all, normally (or is it just novices?), so it makes sense that some of them would end up with "pillow friends".

In a way, I think this aspect of the Tower's culture is there for the purpose of "helping" the women to find their calling. Keeping horny teenaged girls away from men won't change the fact that they are horny teenaged girls, it will just ensure that they look to other horny teenaged girls for a bit of...release. With some, they may find they like it, that they really dislike men altogether, and be more inclined to choose the Red Ajah ("men! yuck! let's hunt them down and kill...err, gentle...them!!". With others, they don't get the girl/girl thing and want to collect men like other people collect socks ("Yay Green! I can have ten men to serve me!!". Others may think the whole sex thing is stupid and go White ("Why would I need a man or woman to satisfy my urges? I have a hand...".

I don't think it's meant to be the deciding factor, by any means (I figure it's just one of many), but by blocking the girls from men during the years where they would most wish to be around them, it likely helps the full sisters get a better idea of who these girls are and which Ajah would be most appropriate for them. After all, you don't want to get a woman in the Red who wants to bond a Warder...you don't want someone who can't look at a man without wanting to throw up or kill him in the Green...you don't want a Yellow that wants fifteen Warders so she can roam the world, and jump in the middle of battles to Heal people.