If I didn't miss anything, the dominated convergence argument turns out to work well. The following shows that $\widehat{G_k}$ can be dominated by a rapidly decreasing decaying function.
Denote $\psi=\widehat{\phi}, \psi_k=\widehat{\phi_k}$, then $\psi_k(y)=2^k\psi(2^ky), \int \psi_k=0$ and $\int |\psi_k|=\int |\psi|$, hence
$$ |\widehat{G_k}(-x)| =|\widehat{\phi_k}\ast G(-x)| =|\int \psi_k(y)G(y+x)dy| =|\int \psi_k(y)[G(y+x)-G(x)]dy|$$ $$=|\int_{|y|\le |x|/2} \psi_k(y)[G(y+x)-G(x)]dy|+|\int_{|y|\ge |x|/2} \psi_k(y)[G(y+x)-G(x)]dy|$$ $$\le \frac{|x|}{2}\sup_{B(x,|x|/2)}|G'|\cdot \int |\psi|+C\int_{|y|\ge |x|/2}|\psi|dy$$
The last line is a function in $x$ decreasing decaying at any rate.
In view of the above argument, the function $\phi$ and $G$ can be replaced by any Schwartz functions where in addition $\phi$ vanishes at $0$, and we will still have $\|\widehat{G_k}\|_1 \rightarrow 0$. An estimate of the rate of convergence decay follows in the specified case.

