I did manage to find a solution, but the odds of it working are probably heavily dependent on how much you change her eyes after applying the Leliana shape.
What I did was to extract the actual hf_genfl_leliana.mor file from the faces.erf file. Then, I created my own morph in the toolset, just accepting that the eye sockets would remain empty as I made my modifications. When I was happy with the changes to her nose, mouth, jaw, etc., I saved the *.MRH, and exported the *.MOR file.
Then, I opened the original hf_genfl_leliana.mor file in the toolset, and opened my own new *.MOR file beside it. Next, I opened up the nodes to find the ones related to eyes. It seems a bit random which node numbers will contain the eye data, but just look for the following tags:
EyesM1
eye_Right
eye_Left
I'm not sure how critical the eye_Right and eye_Left values are, but I just copied the POSITION value from the original hf_genfl_leliana.mor file over to mine. The EyesM1 node seems more important. I did the following...
In my new *.MOR file, I opened the node that was named "EyesM1" (It happened to be node 28 in the tree for my file, but yours will probably be different). Then, I deleted the MESH_STREAM_VERTEXDATA, MORPH_TEXTUREPARAM, MORPH_VECTOR4FPARAM, and MORPH_FLOATPARAM lines. After that, I copied, in order, the same lines from the original hf_genfl_leliana.mor file to mine. I did this by selecting the item, right-clicking, and choosing copy. Next, I went over to my file's tab, clicked on the NUMBER of the node that contains EyesM1, then pasted. If you don't have the node itself selected, you could run into an issue where the value is pasted at a lower subnode spot.
Anyway, after all that, I changed the NAME value (second row down from top of the file) to "hf_genfl_leliana", saved, and copied into the override folder. All that was left to do was rename my file hf_genfl_leliana.mor, and start the game. It seems to work just fine so far. I really just made a few changes to her lips, hair, and jawline, but I'm happy with how she looks now.