Several ways to look at it:
From where are you flying home? If you have to get back to Paris to fly out, then you're probably not spending much to keep the car for a few more days (but also gas and highway tolls to get back to Paris).
If you don't need the car the whole time that you're with friends, that might allow you to cut the rental shorter, offsetting the second-country drop fee. Flights from Zurich or Munich back to Paris can be reasonable; see www.skyscanner.com. In addition to getting price quotes from Auto Europe, also check the price of a 3-week lease through Europe By Car (but since the program is France-based, there can delivery and drop-off fees in neighbor countries). If you fly out from Geneva, for instance, there are car rental offices designated on the French side of the airport, that count as dropping in France, and Basel-Mulhouse airport is actually in France.