First let me say, there shouldn't be a conflict here: The Lord's house is one of order. The Holy Ghost does not encourage you to rebel against God. (When we see what appear to be contradictions to this in the scripture: exceptions, you will note that it is not the individual asking God for an exception, it is the Spirit directing and I can't think of an instance in which the person WANTED to be the exception. For example, Nephi killing Laban. One could also argue he wasn't really an exception since Laban had tried to kill him already and stolen his property. He was justified in self defense.) The Holy Ghost is a second witness.Doctrine and Covenants 1:14-16
"14 And the arm of the Lord shall be revealed; and the day cometh that they who will not hear the voice of the Lord, neither the voice of his servants, neither give heed to the words of the prophets and apostles, shall be cut off from among the people;
15 For they have strayed from mine ordinances, and have broken mine everlasting covenant;
16 They seek not the Lord to establish his righteousness, but every man walketh in his own way, and after the image of his own god,. . ."
Second, in Joseph Smith's day, the Lord's kingdom was not organized on the earth and therefore had to be restored. That is not the case today, so any false correlation between current prophetic counsel to avoid false prophets, in no way conflicts with Joseph receiving revelation and restoring the Church the way he did. Now that it IS organized, there is not a need to restore it again. We just need to live what has already been revealed.