I'm not sure I have completely parsed your question, but it seems to be based on an assumption that the $\sigma$-fields $\mathfrak{F}_1, \mathfrak{F}_2$ are in some sense "orthogonal". That doesn't have to be true; they can even be equal.
Take as an example $\Omega = [0,1]$ with its Borel $\sigma$-field $\mathcal{F}$ and let $\mathbb{P}$ be Lebesgue measure. Note the following fact: if $g : [0,1] \to \mathbb{R}$ is Borel and injective with a Borel left inverse $g^{-1} : \mathbb{R} \to [0,1]$, then $\sigma(g)$, the smallest $\sigma$-field making $g$ measurable, is $\mathfrak{F}$ itself. (Proof: for any Borel set $B \subset [0,1]$, the function $1_B \circ g^{-1} \circ g = 1_B$ is $\sigma(g)$-measurable.)
Let $g_1(x) = x$ and $g_2(x) = x^2 - \frac{1}{2}$. They are orthogonal in $L^2$, so if we let $K$ be the one-dimensional space spanned by $g_1$, we have $g_2 \in K^\perp$. But each is Borel and injective (indeed, each is a homeomorphism onto its image) so we end up with $\mathfrak{F}_1 = \mathfrak{F}_2 = \mathfrak{F}$.
In particular, if $\nu$ is a measure absolutely continuous to $\mathbb{P}$, and $\int f\,d\nu = 0$ for all $f \in L^2(\mathfrak{F}_1)$, then $\nu = 0$.
Basically, the issue is that there are a lot of operations that don't enlarge a generated $\sigma$-field, but do enlarge a subspace of $L^2$. Multiplication is perhaps the most obvious example.