My +1 to put those icons back in the navigation/administration blocks. I don't think we should get rid of them because they don't fit as is in the layout. From a user experience point of view, they are a great asset as they help to quickly track what link you are looking for in a, already very complex, navigation. Not mentioning that this does not only apply to the administration block, but also in the navigation block. When you expand a course section, you'd usually look for the activity icon to quickly find what activity you're looking for.
Regarding the grey colour issue. That shouldn't be an issue as any theme can easily override the images, and as the current images are SVG, it makes it even easier to style them. Of course, you would need to create a few version of them if you want :hover effects. Also, if we're trying to follow Bootstrap logic, I don't think that means that we absolutely have to stick with their default colours. It might be much easier to convert the arrow in the navigation to grey and changing the background color, than overriding each of our icons. Isn't that what LESS is for?
The colour consistency should stay as well, I don't know if that was done on purpose but the icons (from their sprite, or font-color styled) should be consistent with the rest of the core icons. Whatever colour we choose, a lot of effort has been made in 2.4 to create this consistency and we should really work hard in keeping the styles nice and consistent. Or at least have good reasons to change the existing.
Let's not forget about the accessibility issues this represents, an image tag has an alt tag which can be very useful to screenreaders:
// In current code:
<a href="delete.php"><img src="delete.png" alt="Delete" class="icon-delete"></i></a>
// Should become
<a href="delete.php"><i class="icon-delete"></i><span class="screenreaders-only">Delete</span></a>
// or (but I'd say that the above is better)
<a href="delete.php" title="Delete"><i class="icon-delete"></i></a>
That means that the conversation cannot be that simple. And that makes me think that we should do a quick accessibility test on the areas where Simple has define renderers.
As Martin commented above, Ankit has developed a POC of restyling SVG icons on the fly. I imagine we could have CSS rules such as: background-image: url("delete.svg?#000000") who would return a black delete icon, which could be cached and stored so that it becomes a normal file serving once generated. That would act more or less like fonts, except that it still is one more file for the user to download.