To solve this, you can automatize the Maxwell Render task by exporting the .mxs sequence of your scene (1 .mxs per frame), and then batch process directly inside the Maxwell Render standalone application.
First step is set the Maya parameters as usual for an animation: File name prefix, Image format, name.#.ext for your outputfiles, and be sure to set the Frame padding to 4. It´s extremely important you pay attention to this setting or else Maxwell Render will not recognize your files in the batch rendering process later:
Set up your Maxwell settings as you want and select a minimum Sample Level (SL) or time (in minutes) that will be used by Maxwell to achieve the aim for each frame: when Maxwell achieves the the faster option (desired sample level or desired time) it will automatically close/save the render and will begin the render of the next frame:
Go to File > Export all Objects and select File type: Maxwell Scene and be sure to check Animation option. Then press Export All and select where do you want to save all the .mxs files: remeber one .mxs per frame will be saved, maybe a huge amount of data, depending on your scene:
Next step: Open Maxwell Render (standalone aplication) and go to File > Open MXS then select the first .mxs file recently exported in your sequence:
Go to Render Options tab and select the folder where you want to save the .mxi files and output images. Finally, set the your animation frames range (in this example, from 1 to 100):
Finally hit render, and... that´s it!: your batch render process will start immediatelly and you´ll have not to warry about render frame by frame your Maya sequence using Maxwell Render.
Note: I´ve been testing a few times this method, and it uses to works fine, but if you try to apply 'shake movement' to the camera via expressions, unfortunately the .mxs conversion process will not recognize the code and the camera will not achieve the desired effect.