Is there any way to skip the line?
What line?
Security ---NO
You have to go through security which never can be skipped and can be lengthy.
Yes, if you are interested--and can get tickets--if you first take the Scavi tour. At the end of the tour you just walk up internal stairs to the Basilica. You can learn more here: https://www.youtube.com/watch?v=JfBlqsU91Pc