First of all, I would like to say that I really enjoyed the movie, which, in all of its weirdness and cynicism i think it can still be defined as a romantic comedy of sorts, which is rare to find (the first other example that comes to mind is Eternal Sunshine of The Spotless Mind)
About your questions:
In short I guess they're showing that our society is cruel to single people and we encourage to live together.
In the first part of the movie this is clearly shown, but as David (Farrell) escapes the "resort" in which he was forced to enter, he finds himself between the group of singles which are not less fiercely ideological than the mated ones.
the loner group (...) has some rules which basically means no relationship. WHY? Aren't they all ran off to become independent? Then why single people are putting cruel rules on themselves? What does it mean?
It means that there is no real difference between the two groups since both blindly apply the same fundamentalist approach, although it leads them to behave in opposite ways. The director's critic, in my opinion, is meant to address the society as a whole or at least those who are always thinking in terms of absolutes, not just the people that think that a single is a loner (or a loser).
And why loner leader Léa Seydoux is so desperate about rules that she blinded Rachel Weisz. What's the hidden meaning of this character loner leader?
It is not clear to me whether she's acting out of spite (jealousy) because of the relationship between David and "The Short Sighted Woman" or because she wants to punish her for breaking their "law". When the loner leader finds the Short Sighted Woman's diary and reads it realizing her betrayal, I thought I saw a glimpse of envy in her, but maybe it was just my imagination.
Whatever the reason, the loners are trying to distinguish themselves as much as they can from the others, therefore, if the society strongly encourages (so to speak) people to live as a couple, they need to rebel to this rule and live by contrast.
Also, since the coupling of people in this dystopic society is based on the matching of their defects (see the limping guy that causes himself nosebleeds in order to be considered as the perfect match for the nosebleeding girl), the loner leader thinks that the best way to disrupt the relationship between David and the Short Sighted Woman is to blind her, thus cancelling what they have in common.
Here in the US Variety online edition there is an interesting review of the movie in which many cues for reflection can be found.
Hope this answers your doubts