I could not find a solution with raw files, I know the recent version of hugin is supposed to support raw files using dcraw but I cannot test it myself. The next good solution in my opinion is to convert all of your raws to tif files or other lossless image format and use them.

For my method I mainly hugin_tools on the terminal but I also use the GUI so keep in mind you need both installed. You can find the hugin suit here for download. Also I am using Ubuntu on my machine but the procedure on mac should be the same.

First thing you need to put all the photos in one folder, this is mainly for convenience' sake but will help with the commands later.

Generate a pto file

Next you need to generate a pto file, that is the file where all the image transformation data is saved. You can do so by typing:

pto_gen *.jpg

in the terminal where all the photos are.

Cropping to still area

Now you need to find matches between all of your images, before you do that there is an optional part which will greatly reduce errors if there are moving objects in your set.

Open the hugin project you generated and change the interface to advanced.

In the window that opened go to the masks tab and there chose the crop tab and select your first image. Now make sure 'all images of selected lens' is checked and then drag from the edges of the image and crop to the area with the least or no amount of movement. This will constrict the match finder to that area and reduce error in the remapping stage. Now you can save and exit the program.

Finding control points

Now you can find the matches, type:

cpfind --linearmatch *.pto

into the terminal, this will find matches between pairs of images. You can also find matches between all images by simply omitting the ‘linearmatch’ option but if you have hundreds of images it will take a very long time and is also probably unnecessary. You can learn more about cpfind here.

Next you need to clean the control points you found, there are two commands for that purpose:

celeste_standalone -i default.pto -o default.pto

will try to erase control points on clouds (More information here). And

cpclean -o default.pto default.pto

will remove control points with high error value. (cpclean help page)

Reset crop

Now that we are done with control points open the new generated project called default and head back to the masks tab like before, here select the crop tab again and click the reset button, this will disable the crop from all the images.

Optimizing

After that you need to optimize the control points. Type:

pto_var --opt="y, p, r, TrX, TrY, TrZ" -o default.pto default.pto
autooptimiser -n -o default.pto default.pto

That will optimize the position and distortion of your image set, you can learn more about this process here.

You are almost done, now just type:

pano_modify -o default.pto --projection=0 --fov=AUTO --center --canvas=AUTO --crop=AUTOHDR --output-type=REMAPORIG default.pto

to change the project configuration.

Remmaping

Lastly just type:

nona -m TIFF_m -o remapped default.pto

to output the remapped images. If you want to also stack the images together you can also use:

hugin_stacker --output=median --mode=median remapped*.tif

More information about hugin command-line tools can be found here.

That's it, that my take on your problem, there are a few missing links because this is my first answer so i was limited to 8. If there are any mistakes or you have any problems please let me know, also my English is not the best so sorry if I made any grammar or spelling mistakes. Cheers!