The standard argument to get the expected number of bins occupied is greatly simplified by the linearity of expectation. We only need to compute the probability that a single bin is filled. This is simplified by computing the probability that that bin is empty: $\left(1-\frac1n\right)^m$. Thus, the probability that that bin is filled is $1-\left(1-\frac1n\right)^m$. Linearity of expectation says that the expected number of bins filled would be
$$
n\left(1-\left(1-\frac1n\right)^m\right)\tag{1}
$$
as you have stated.
However, when assuming that at least $k$ bins have been filled, we can not use all of the preceding simplifications.
Inclusion-Exclusion
One method of attack is using the Inclusion-Exclusion Principle. Let $S(i)$ be all the possible arrangements where bin $i$ is empty. Then we can compute $N(k)$, the size of the intersection of $k$ of the $S(i)$: there are $\binom{n}{k}$ ways to choose the empty bins and $(n-k)^m$ ways to put the $m$ marbles in to the remaining bins. Therefore,
$$
N(k)=\binom{n}{k}(n-k)^m\tag{2}
$$
Now, to compute the number of arrangements in which exactly $k$ bins are filled, we compute the number of elements in exactly $n-k$ of the $S(i)$:
$$
\begin{align}
&\sum_{j}(-1)^{j-n+k}\binom{j}{n-k}N(j)\\
&=\sum_{j}(-1)^{j-n+k}\binom{j}{n-k}\binom{n}{j}(n-j)^m\\
&=\sum_{j}(-1)^{j-n+k}\binom{k}{j+k-n}\binom{n}{k}(n-j)^m\\
&=\binom{n}{k}\sum_{j}(-1)^{k-j}\binom{k}{j}j^m\tag{3}
\end{align}
$$
The number of ways to get at least $k$ bins filled is
$$
\begin{align}
&\sum_{i\ge k}\sum_j(-1)^{i-j}\binom{n}{i}\binom{i}{j}j^m\\
&=\sum_i\sum_j(-1)^{k-j}\binom{-1}{i-k}\binom{n}{j}\binom{n-j}{n-i}j^m\\
&=\sum_j(-1)^{k-j}\binom{n}{j}\binom{n-j-1}{n-k}j^m\tag{4}
\end{align}
$$
The number of bins times the number of ways to get at least $k$ bins filled is
$$
\begin{align}
&\sum_{i\ge k}\sum_j(-1)^{i-j}i\binom{n}{i}\binom{i}{j}j^m\\
&=\sum_i\sum_j(-1)^{k-j}i\binom{-1}{i-k}\binom{n}{j}\binom{n-j}{n-i}j^m\\
&=\sum_i\sum_j(-1)^{k-j}[k+(i-k)]\binom{-1}{i-k}\binom{n}{j}\binom{n-j}{n-i}j^m\\
&=\sum_i\sum_j(-1)^{k-j}\binom{n}{j}\left[k\binom{-1}{i-k}-\binom{-2}{i-k-1}\right]\binom{n-j}{n-i}j^m\\
&=\sum_j(-1)^{k-j}\binom{n}{j}\left[k\binom{n-j-1}{n-k}-\binom{n-j-2}{n-k-1}\right]j^m\tag{5}
\end{align}
$$
Dividing $(5)$ by $(4)$ yields the expected value
$$
k-\frac{\sum\limits_{j=0}^n(-1)^{k-j}\binom{n}{j}\binom{n-j-2}{n-k-1}j^m}{\sum\limits_{j=0}^n(-1)^{k-j}\binom{n}{j}\binom{n-j-1}{n-k}j^m}\tag{6}
$$
where $\binom{-1}{k}=(-1)^k$ and $\binom{-2}{k}=(-1)^k(k+1)$ and $0^0=1$.
Example
For $n=6$, $m=4$, $k=2$:
$$
\begin{align}
&2-\frac{\small\binom{6}{0}\binom{4}{3}0^4{-}\binom{6}{1}\binom{3}{3}1^4{+}\binom{6}{2}\binom{2}{3}2^4{-}\binom{6}{3}\binom{1}{3}3^4{+}\binom{6}{4}\binom{0}{3}4^4{-}\binom{6}{5}\binom{-1}{3}5^4{+}\binom{6}{6}\binom{-2}{3}6^4}
{\small\binom{6}{0}\binom{5}{4}0^4{-}\binom{6}{1}\binom{4}{4}1^4{+}\binom{6}{2}\binom{3}{4}2^4{-}\binom{6}{3}\binom{2}{4}3^4{+}\binom{6}{4}\binom{1}{4}4^4{-}\binom{6}{5}\binom{0}{4}5^4{+}\binom{6}{6}\binom{-1}{4}6^4}\\
&=2-\frac{0-6+0-0+0-(-3750)+(-5184)}{0-6+0-0+0-0+1296}\\
&=\frac{670}{215}\doteq3.11627906976744
\end{align}
$$
whereas, without the knowledge that at least two bins were not empty, we would get
$$
6\left(1-\left(1-\frac16\right)^4\right)=\frac{671}{216}\doteq3.10648148148148
$$
Not a terribly large difference, but with $4$ balls into $6$ bins, you wouldn't expect them to all land in one bin, so the knowledge that at least two bins were not empty is not very significant.
