If you do not want to perform any net surgery, you have to use a three channel input. You can either (i) repeat copies of your grayscale images or (ii) pad them with zeros. For example, you can do the following in MATLAB:
(i) X = repmat(X, [1 1 3]);
(ii) X = padarray(X, [0 0 2], 'post');
where X is a grayscale image. See Section 3.4. in
http://arxiv.org/abs/1503.08909 for an example of finetuning a three channel model on two channel inputs. tl;dr they use (ii).