I searched the forum and see multiple threads about request for navigation to be support inside lightbox for Galleria, however the respond was always there was no need to because you can navigate with the thumbnail.

That may be true for a horizontal gallery with small height. But when you have the gallery in a vertical style that fills a small area or pop up window, it becomes very stupid to have to have to scroll all the way down to find the thumbnail then scroll all the way back up again to view the image. Repeat that four to five times and it gets seriously annoying.

But since there are no intention to add navigation in for Galleria's lightbox. Would it be possible to have an option or help on how to disable the pop up engine for Galleria? It's ridiculous to get complains/feedbacks that lightbox navigation is not working, only to be able to reply that its not a bug, that's how it works.

I search the forum and pulled up an old article where someone once requested the to disable the popup engine as well.
forum.joomlaworks.net/simple-image-gallery-pro-%28plugin%29/how-to-disable-entire-pop-up-mechanism/msg63027/#msg63027

However following the steps from that link, I still get a pop up clicking on the large image. Seems deleting rel="[code here]" attribute causes the plugin to default to something else that pops up in a new window. My guess is something changed in the new version of the plugin since then, so is there a new step to disable PopUp Engine?

You should override your template. Take a look at the documentation for more  about overriding templates.
What you should modify is change this in plugins\content\tmpl Galleria\default.php

<a href="<?php echo $gallery[0]->sourceImageFilePath; ?>" class="sigProGalleriaTargetLink<?php echo $extraClass; ?>" rel="<?php echo $relName; ?>[gallery<?php echo $gal_id; ?>]" title="<?php echo $gallery[0]->captionDescription.$gallery[0]->downloadLink.$modulePosition; ?>" target="_blank">
                <img class="sigProGalleriaTargetImg" src="<?php echo $gallery[0]->sourceImageFilePath; ?>" alt="<?php echo JText::_('JW_SIGP_LABELS_08').' '.$gallery[0]->filename; ?>" title="<?php echo JText::_('JW_SIGP_LABELS_08').' '.$gallery[0]->filename; ?>" />
            </a>

to this:

<a href="#" class="sigProGalleriaTargetLink" rel="<?php echo $relName; ?>[gallery<?php echo $gal_id; ?>]" title="<?php echo $gallery[0]->captionDescription.$gallery[0]->downloadLink.$modulePosition; ?>" target="_blank">
                <img class="sigProGalleriaTargetImg" src="<?php echo $gallery[0]->sourceImageFilePath; ?>" alt="<?php echo JText::_('JW_SIGP_LABELS_08').' '.$gallery[0]->filename; ?>" title="<?php echo JText::_('JW_SIGP_LABELS_08').' '.$gallery[0]->filename; ?>" />
            </a>

If this doesn't work, remove

rel="<?php echo $relName; ?>[gallery<?php echo $gal_id; ?>]"

too.

<a href="<?php echo $gallery[0]->sourceImageFilePath; ?>" class="sigProGalleriaTargetLink<?php echo $extraClass; ?>" rel="<?php echo $relName; ?>[gallery<?php echo $gal_id; ?>]" title="<?php echo $gallery[0]->captionDescription.$gallery[0]->downloadLink.$modulePosition; ?>" target="_blank">
                <img class="sigProGalleriaTargetImg" src="<?php echo $gallery[0]->sourceImageFilePath; ?>" alt="<?php echo JText::_('JW_SIGP_LABELS_08').' '.$gallery[0]->filename; ?>" title="<?php echo JText::_('JW_SIGP_LABELS_08').' '.$gallery[0]->filename; ?>" />
            </a>

The code disables the pop up engine but it still opens a new window cause of target="_blank" so I changed that to _self, however because my gallery appears in a pop up already, it still causes a redirect. Also the code breaks the linking when I click on the thumbnail. After clicking on the thumbnail to change the image, clicking on the enlarged image would just become a direct link to the image itself.

Would it be possible to just remove the hyperlink so it can't be click on in the first place?

Did you try removing:

rel="<?php echo $relName; ?>[gallery<?php echo $gal_id; ?>]"

too?

Yes I removed that as well. Tried both the code you suggested.

I also tried removing <a href=" and </a> so there would not be a hyperlink to click on but that cause the thumbnail to be unable to load in the large placeholder when clicked on.

Yes I removed that as well. Tried both the code you suggested.

I also tried removing <a href=" and </a> so there would not be a hyperlink to click on but that cause the thumbnail to be unable to load in the large placeholder when clicked on.

I am interested in a solution as well.

As far as i can tell, the related script BEHAVIOR.JS is written specifically for the Galleria layout markup. In other words, it relies on the <a>-Tag. Galleria click-on-thumb functionality will break if one or the other file is modified.

Anyone can solve this?