This is not necessarily true, unless there is some finiteness condition like $R$ being noetherian. I will give a proof assuming $I$ is finitely generated, and a counterexample otherwise.
Let $N=\frac{M}{\Gamma_I(M)}$, and $x\in \Gamma_I(N)$. That means $\exists n \geq 0$, such that $x\in \text{Ann}_N(I^n)$. By definition, this means $I^nx=0$ in $N$. The problem is to show $x=0$.
Let $y\in M$ be an element that maps to $x$ under the quotient homomorphism $M \rightarrow N$. Then $x=0$ if and only if $y \in \Gamma_I(M)$. Therefore the problem is to prove if $I^n y \subset \Gamma_I(M)$, then $y\in \Gamma_I(M)$.
$I^n y\subset \Gamma_I(M)$ means for every $r\in I^n$, there exists some $k$ (depending on $r$) such that $ry \in \text{Ann}_M(I^k)$, i.e. $I^kry = 0$. We want to show $I^m y=0$ for some $m \geq 0$.
If we know that $I^n$ is finitely generated (for example if $R$ is noetherian), we may proceed as follows. Pick generators $r_1,\dots ,r_s$ for $I^n$. For each $r_i$, there exists $k_i \geq 0$ such that $I^{k_i}r_i y = 0$. Let $k=\max_{1 \leq i \leq s} k_i$, so that $I^kr_iy = 0$ for every $i$. Then for every $r\in I^n$, $r=a_1 r_1 + \cdots + a_s r_s$ for some $r_i \in R$, and
$$I^kry = I^k(a_1 r_1 + \cdots +a_s r_s)y = a_1 I^kr_1y + \cdots +a_s I^kr_s y=a_1.0+\cdots +a_s.0=0.$$
Then $I^kry=0$ for every $r\in I^n$, so $I^{k+n}y=I^k I^ny = 0$. Thus $y\in \text{Ann}_M(I^{n+k})\subset \Gamma_I(M)$, and so $x=0$ in $\frac{M}{\Gamma_I(M)}$, and we are done.
For a counterexample in general, let $R=\prod_{n=3}^\infty \mathbb{Z}/2^n\mathbb{Z}$, and let $R_0$ to be the ideal $\oplus_{n=3}^\infty \mathbb{Z}/2^n\mathbb{Z}$ of eventually-zero vectors in $R$. Take $M=R$, and $I=2R_0$. The element $y=(1,1,1,...)$ in $M$ does not belong to $\Gamma_I(M)$, since for any $n\geq 0$, $I^n y=I^n \neq 0$. But in fact $Iy \subset \Gamma_I(M)$. Indeed, if $r=(r_1,r_2,\dots ,r_s,0,0,...) \in I$, then $ry =r$ is annihilated by $I^{k}=2^kR_0$ whenever $2^k \geq s+2$, so that $ry \in \text{Ann}_{I^k}(M)$, and $Iy\subset \Gamma_I(M)$. In this case $\Gamma_I(M)=R_0$, and two vectors $y_1,y_2\in M$ map to the same element in $M/\Gamma_I(M)$ if and only if they are equal almost everywhere. Since any vector in $M$, once multiplied with an element of $I$ is zero almost everywhere, we have
$$\Gamma_I\left(\frac{M}{\Gamma_I(M)}\right)= \text{Ann}_I\left(\frac{M}{\Gamma_I(M)}\right)=\frac{M}{\Gamma_I(M)}=R/R_0\neq 0.$$