Apples and oranges.
The resolution clearly says that the Senate is thanking him for his service as an officer of the Senate. There's nothing controversial there, it's honoring Thurmond's *current* service.
Lott's remarks are controversial because he (twice) said that the country would have been better off if Thurmond had won the presidency back in 1948, WHEN THURMOND WAS A STRONG SEGREGATIONIST. By specifically referring to the 1948 run both times, Lott was, intentionally or not, expressing approval for the "good old days" of segregation.
He was referring to the man he came to know and admire in Washington DC, a man far removed from 1948 SC.