High-side switch Vs Complete mosfet push-pull configuration to drive an inductive load
I need to evaluate two kinds of designs: The first one, which is a complete mosfet based push-pull configuration with an LC filter to linearize the PWM.


This isn't actually a push-pull design. The lower FET never pulls. Current always flows through it from source to drain, not drain to source. 

This configuration is usually called an "active switch" configuration. Because the lower FET is replacing the diode of your second design.


  What are the benefits/drawbacks of one configuration over the other?


The active switch design can be more efficient. The diode based design is likely to be less expensive. Exactly as you already determined.

Deciding which is best for you will depend on the exact balance of the importance of cost and efficiency in your application. And it how well you can optimize it will depend on all the detailed choices you make in designing either of the two choices, and your ability (or your organization's ability) to find good prices for the different types of components.

Unfortunately (or fortunately) there are thousands of different controller chips, MOSFETs, and diodes out there to choose from, and pricing changes dynamically so it's unlikely you'll ever find the absolute best choice.

Edit: As another answer points out, either one of these is probably overkill (and excess cost) to solve your actual problem. The fan itself can be used as an inductive element to smooth a PWM signal. Or, if the reason you want "no unfiltered PWM" is to reduce audible artifacts, finding a controller that can provide a higher PWM frequency may be the most cost-effective solution.