A few things to consider:
1. If it saves you money, pay it off.
2. You will still have another auto trade line so you should be OK there....
3. I found that anytime I pay off an installment tradeline I get a few point ding but nothing drastic and the effect is transient.
4. Keeping the longer auto loan open will be better than paying it off as you should have a higher percentage paid off. But see #1 when it come to deciding.
Good luck...
