JOEL - From what I have read it is hard to be certain what are historical facts and historical fiction when it comes to Columbus' character and the things he did. Unfortunately many past historians were somewhat overenthusiastic in their attempts to disgrace Columbus, serving to advance their own political cause rather than represent the truth.

The Book of Mormon scripture in question says:

"And I looked and beheld a man among the Gentiles, who was separated from the seed of my brethren by the many waters; and I beheld the Spirit of God, that it came down and wrought upon the man; and he went forth upon the many waters, even unto the seed of my brethren, who were in the promised land." (1 Nep 13:12)

This scripture only tells us that the spirit inspired Columbus to decide to go upon the many waters. It doesn't say that the spirit was always with him during or after the voyage.
Through His spirit God can inspire anyone to do good things to serve His purposes, even when most of the rest of the time they might not be such nice people. The apostle Paul(Saul) in the Bible is a good example of God inspiring a seemingly wicked person to do something good (Acts 7:57-60; Acts 8:1-3; Acts 9:1-2: Acts 9:3-6).
Despite his human weakneses and character flaws, Columbus was convinced that he possesed gifts from God that were the key to his success:

"He(God) bestowed the arts of seamanship upon me in abundance, and has given me what was necessary from [astronomy], geometry, and arithmetic; and has given me adequate inventiveness in my soul ... encouraging me to go forward, and without ceasing they inflame me with a sense of great urgency."
(Columbus to Doña Juana de la Torre, Raccolta di documenti e studi pubblicati della R. Commissione Colombiana, pt. I, vol. ii; I Scriti di Cristoforo Colombo, ed. Cesare de Lollis (Rome: 1894), p. 82.)

He also gave God the glory for what he or anyone can accomplish:

"The eternal God our Lord gives to all those who walk in his path victory over things that seem impossible. And this is notably one; for, although men have talked or written of these lands, all has been conjecture. All Christendom ought to feel delight and make great feasts and give solemn thanks to the Holy Trinity with many solemn prayers for the great exaltation they shall have in the turning of so many people to our holy faith."
(Cristóbal Colón, Textos y documentos completos: Relacionesde viajes, cartas y memoriales, ed. Consuelo Varela (Madrid: Alianza Editorial, 1989), pp. 137-38.)

Columbus believed he was an instrument in God's hands to carry out his project:

"the Lord opened my mind to the fact that it would be possible to sail from here to the Indies, and he opened my will to desire to accomplish the project. Who can doubt that this fire was not merely mine, but also the Holy Spirit who encouraged me with a radiance of marvelous illumination from his sacred Scriptures."
(Libro de las profecias, p. 105. Raccolta, pt. I, vol. ii, p. 79.)

However history remembers the man, the historical fact remains that Columbus helped make it possible for people to come to a land where they would be free to worship God as they pleased, providing an ideal situation for the gospel of Jesus Christ to be restored to the earth.