In my opinion, if you are staying for just two days in Kathmandu, then it makes sense to go for a Pashupatinath tour package because apart from being a tourist attraction, Pashupatinath is also one of the most sacred Shiva temples on the Indian subcontinent. The spiritual vibes near the Bagmati River, despite being non-religious yourself, are worth experiencing during the evening aarti. It feels like an experience from a movie scene to witness chanting, lights, smoke, monkeys creating a nuisance, and people praying.
Moreover, almost all tour packages also visit Guheshwori Temple, Jal Narayan & Shwambhu Nath Temple to cover the spiritual attractions in one go without wasting your time understanding the traffic in Kathmandu.
I went to Pashupatinath via Ojas Travel, and what I loved was the way our guides used to explain the rituals without making it a history lesson in school. In addition to that, they also had a knack for standing at the right spot for the aarti without being pushed away by the crowd.
Overall, it was definitely worth the effort.