There are apparently lots of regional/local rental car companies in Croatia that get
good reviews, look backwards in the forum. But going into a different country may
trigger additional fees and such as noted.
Renting from Sixt is no hassle, but no matter what, taking pictures of the car before
you take it out is the best way to have data to contest any assertion of damage.
Without any additional information on your itinerary, another option is to rent from
Split to Zagreb, drop off the car/spend a little time in Zagreb, then take a 2 hour bus
to Ljubljana, see Ljubljana, and then rent again.
If you do set it up as a single rental, make sure you purchase a tollway vignette
for Slovenia or any other country to drive the car into.