Despite what you've probably heard, Silicone isn't terrible for side seams and windows - it's just the roof where it becomes problematic. Several RV manufacturers use silicone around window frames, for example.
But you can avoid the question by using a product like Geocel Proflex RV or one of the 3M Body Seam Seal variants (often available in auto parts stores). Amazon or Ebay is a good source for either of those as well. The Proflex is available in several colors, but I think the 3M is clear only.
2004 American Tradition; 2014 Buick LaCRosse
Homebase in the Ocala Nat'l Forest near Ocala, FL