Did the finding of the electron from cathode rays/ oil drop experiment at least temporarily throw Dalton's Atomic theory "out the window"?
Dalton's theory was about how atoms behaved: the observation of Cathode rays provided part of the explanation of why they behaved like this

The key elements of Dalton's theory were observational. He explained how the idea of atoms could explain chemical reactions and many observational facts about them. This was an important breakthrough and explained far more than previous ideas. But it didn't provide much of an explanation of why they behaved that way.

The observation of cathode rays was one of the first steps in providing the why not a fundamental challenge to Dalton's actual theory. Chemists didn't get a (mostly) complete explanation of what atoms behave the way they do or of some of the characteristic features of atoms until the discover of the neutron in the 1930s. Why, for example, do atomic weights not always follow the atomic numbers (or the pattern of chemical behaviour observed across the periodic table)?

We now understand that chemical properties are determined by the electrons in atoms and the number of electrons depends on the number of nuclear protons. But the mass also includes neutrons which occasionally alters the apparent periodic relationship between atomic mass and chemical properties.

None of this is a fundamental challenge to Dalton's ideas. All of it is a deeper explanation of why the observed properties and behaviours of atoms in Dalton's theory work as they do. 

So we didn't throw Dalton's ideas out. We refined them with a more fundamental theory that explained why they behave like that. 

This contrasts with other changes in our understanding of chemistry. For example, we discarded the old phlogiston theory of the explanation for combustion because observations didn't refine it but completely refuted it.