This is a good question,
More or less most of the sects of Hinduism are in accordance with the Vedas.
You are right that Vedas focus more on the Vedic deities viz. Indra, Surya, Aditya, Agni, Prajapati, Varuna, Mitra etc. but the worship of these deities have declined in the past few centuries.
Many are of the opinion that when Puranic deities became popular it affected the popularity of Vedic deities and people shifted to Puranic deities and puranic rituals which are relatively less complex than the Vedic.
Vedic dharma refers to following the tenets of the Vedas and living the life accordingly.
To lead a life as prescribed by the Vedas, here is the system to be followed by one and all:
Initiation into Gayathri Upasana
Study of the Vedas or understanding the messages given in them.
Agni upasana as part of Gayathri Upasana and vedic study (BRAHMACHARYA).
Getting into married life and continuing Agni Worship as a couple – Grahastha Dharma.
Offering one’s body in the fire worshipped by the couple (The concept behind the ritual followed for cremation in the present day)
Sanatana Dharma is usually used as a synonym to the Vedic dharma. Hinduism is more of a broader term which has more focus on gee-cultural aspects. Hence Hindus means those who belong to the region around Sindhu river. There are many sects which have emerged in India.
Presently there are some sects like Veerashaiva and kapalika which do not directly subscribe to Vedas but consider the respective agamas as the final authority. However, the principles are more or less related to the Vedas.
In the past, Vratyas and people from Charvaka sect were considered as non-vedic. Vratyas were group of wandering tribes with no specific religion or well organized rules. Charvaka was the materialism centered sect which gave utmost importance to materialism and did not bother about hell or heavens.
There were shramanic people too who existed during Vedic era and later they developed as non hindu sects like Jainism and buddhism.