You don't understand what the Torah is saying. Once a person IS a convert, they are to be treated as any other Jew...
But UNTIL they become converts, they are to be discouraged. There are very good reasons for this--
1) A gentile is NOT required to keep the Law. If the gentile is righteous, s/he will still have a part in the world to come. Once a person becomes a Jew, though, they are obligated to keep the Law--and we believe that they are held accountable to G-d if they do not. IOW, a gentile has much to lose by converting, and should stay as they are if at all possible.
2) Jews have, throughout history, been persecuted in the most horrible of ways. We want to make sure, without question, that a person who converts knows what they're in for if they join up with us. Remember, again, that we don't believe gentiles HAVE to convert in order to enter the world to come. Again, a potential convert has much to lose.
3) At certain points in history, Jews were killed for allowing converts. This tended to discourage the practice. :/
There are other reasons, but these are three of the main ones.
But the problem with your question is that you don't understand what Torah is saying. AFTER a person converts, they are fully accepted. Beforehand, they are discouraged. The common practice is to turn a gentile away three times. If they come back, the rabbi begins to realize that this is a person whose soul is Jewish.
A person who goes through a full conversion process--which can take years--and totally commits to the Jewish people, is to be accepted unequivocally as a Jew.