It was contestible and contested.
I'd ask by whom, but individual names aren't that helpful.
So was the theory of evolution in 1859, and not for obscurantist reasons, or, in the case of evolution, even for unscientific ones.
True, but, both atomic theory and evolution were accepted by 1910, and the former had a 100 year head start on the latter.
Until the atomic theory of matter had been demonstrated beyond reasonable doubt, which it hadn't until Einstein came along, people were free to doubt it for whatever reason they liked, without being accused of obscurantism.
As I said, atomic theory had been demonstrated
before Einstein's time. Richard Lambing was postulating on the structure of the atom in the 1830s, and the flow of
subatomic particles was the prevalent theory of electricity in the 1870s. Hittorf was well aware of atoms and molecules when he conducted his experiments into electricity - in 1879, he was explaining the curvature of electron beams by way of
negatively-charged molecules. If atomic theory was widly contested in the early 1900s, what were all these physicists doing experimenting on things that, according to you, were unproven to even exist?
No, atoms were a fact of science from the early 1800s; the experiments conducted in the 1800s demonstrate this, as does the terminology used by scientists as early as the turn of the century (the 19[sup]th[/sup] century, that is). They knew atoms exist, just as we know they exist today.