Think of the category of structures in some signature $\Sigma$. The functor represented by a finitely presentable object $F$, say, corresponds to some term in the language generated by $\Sigma$. For example, suppose that $\Sigma$ is the signature for fields, and $F = \mathbb{Q}[x]/(f(x))$ for some irreducible polynomial $f(x)$. Then a morphism $F \to K$ corresponds to an element $\alpha \in K$ satisfying the equation $f(\alpha) = 0$. Let $I$ be the initial structure in this language. If $\phi: K \to L$ is a morphism, then to say that $\phi$ is $\omega$-pure with respect to the morphism $I \to F$ is to say the following: if $f$ has a root in $L$, then it already has a root in $K$. So this says that the morphism $K \to L$ reflects satisfaction of the formula $\exists x f(x) = 0$.
Using morphisms $F_1 \to F_2$ where $F_1$ is not initial, we can do something similar for formulas with parameters in $K$. For example, suppose that $F_1$ is the field $\mathbb{Q}[x] / f(x)$ and $F_2$ is the field $F_1[y] / g(x,y)$ for some polynomial $g$. Then $\omega$-purity with respect to the inclusion $F_1 \to F_2$ says that if $\alpha$ is a root of $f$ in $K$, and if there is a root of $g(\alpha,y)$ in $L$, then there is already a root of $g(\alpha,y)$ in $K$.
So basically, purity of a morphism $K \to L$ means that certain types of existence statements, if satisfied in $L$, are already satisfied in $K$. This says that there is a "reflection principle" for the inclusion $K \to L$: if you can solve an equation in $L$, then you can already solve it in $K$. This doesn't say that $K \to L$ is an elementary embedding, but it does say that the map is elementary with respect to some $\Sigma_1$ formulas.