Only God knows what was really going on in your uncle's mind, of course, and God alone is his final judge. The Bible tells us to "judge nothing before the appointed time; wait till the Lord comes. He... will expose the motives of men's hearts" (1 Corinthians 4:5).
I can't help but wonder, however, if your uncle was finally facing the fact that he'd been on the wrong road in life, and was unprepared for eternity. In other words, instead of being hypocritical, his instructions may have been his way of telling you that he'd finally realized his need of God, and had turned to Jesus Christ for the forgiveness he needed. Although your uncle had resisted God all his life, God still loved him and wanted to welcome him into heaven -- and as he approached death he may have realized this.
Whatever his true motives, your uncle's situation should remind us of two very important truths. First, it reminds us of the danger of delay -- of thinking we can leave God out of our lives and then turn to Him at the last minute. But we may never have that "last minute"; death may come suddenly and without warning. The Bible says, "Now is the day of salvation" (2 Corinthians 6:2).
But your uncle's situation reminds us of another great truth: God loves us, and He will forgive absolutely anyone who truly turns to Christ in repentance and faith. Have you put your life into His hands?