Intuition about the first isomorphism theorem
I understand the Theorem in the same way as you. The idea with a lot of these Algebra Theorems, where we factor an algebraic structure through a quotient, is to remove some undesirable part of the structure.
In this case, we want to get an isomorphism out of a surjective homomorphism, which is a much "nicer" map. So, we quotient out by the kernel, and as a result we have a map where only the zero element is sent to zero, which maintains surjectivity.
This sort of Theorem reappears frequently, and yours is the correct intuition.
The fiber point of view is the one I like, because it captures the idea that when you quotient out $ker\phi $, you identify through $\sim $ all the points that $\phi $ sends to $0$.
To extend this a bit, suppose we take a topological space $X$, a space $Y$ and an $f:X\to Y$, and topologize $Y$ by declaring that $V$ open in $Y$ $\Leftrightarrow f^{-1}(V)$ open in $X.$
Now given any $\sim $ on $X$, $q:X\to X/\sim $ induces a topology on $X/\sim $ as above and from this you get the following result:
if $g:X\to Z$ is continuous, then there is a unique $\ \overline g:X/\sim \to Z$ such that $\overline g\circ q=g$
and so we have a topological analog of the First Isomorphism Theorem.