That is mostly true, but the founder Prithvi Narayan Shah did proclaim that Nepal as an official Hindu kingdom.
He was distrustful of Indians because it was under the established Muslim Mughal and the expanding British rule, which he saw as a Christian rule. When he conquered Kathmandu(back then Kathmandu valley was 3 kingdoms), he sent both Muslims and Christian missionaries packing to India.
Although Christian schools, such as St. Xavier's, and churches for local Christians were allowed by the King, it wasn't until the 1990 reform that mosques were allowed to be built within the valley. Today there is a large mosque. Ironically, it was almost destroyed by a mob when a dozen of Nepalese laborers were slaughtered in Iraq by the terrorists.
Raging mob destroying the Kathmandu mosque