The average (centroid) $\lambda = \frac{\lambda_1 + \dots + \lambda_k}{k}$ minimizes the sum of squared differences $f(\lambda) = \sum_{i=1}^k (\lambda - \lambda_i)^2$.
This suggests an algorithm, which is essentially what Louis Deaett suggests, if I understand correctly:
- compute the diagonalization $\Omega = V\Lambda V^{-1}$.
- permute eigenvalues and eigenvectors so that the sum of squared distances from the centroid $f(\lambda)$ is minimized by the first $k$ eigenvalues. It is not clear how to do this step in optimal time, even if the solution may be evident in the 'eyeball norm' in many practical cases.
- replace those $k$ eigenvalues with their mean, to obtain $\tilde{\Omega} = V\tilde{\Lambda}V^{-1}$.
I conjecture that this algorithm gives you the optimal answer in the Frobenius norm $\|\Omega - \tilde{\Omega}\|_F^2 = \sum_{i,j} (\Omega_{ij} - \tilde{\Omega}_{ij})^2$; based on experience on similar problems, it looks like Weyl's inequalities for eigenvalues could be used to give a proof.