Yes, there are some alternative access points in the Jomsom Trek apart from the Naya Pul. Either you could reach Birethanti or Tatopani and join the Jomsom trek route.
You could walk from Pokhara to Birethanti. By walking through Sarangkot, you can reach Naudanda. From Naudanda, follow the road for sometime, turn off past Khare to Chandrakot and then descend to Birethanti.
You can also take a bus to Beni, further northwest of Pokhara, and avoid the long climb over the Ghorepani hill. From Beni, you can take a two day trek to Tatopani and join the Jomsom trek.
Read Jomsom Trekking for comprehensive itinerary.