Changing how pasted returns are handled

I'm trying to fix an issue I have with Wordpress 3.9, and CKEditor was suggested to me as one possible solution. It doesn't look like it fixes the problem out of the box, but since it looks like there are a lot of customization options, it seems like there might be a way to do what I'm looking for, if I can just figure out how.

Here's the issue: I deal with a lot of text that's copied and pasted from other applications, primarily InDesign.  When I paste in a block of text from an InDesign document, which has a single return between each paragraph, I get this:

<p>This is the first paragraph.<br />This is the second paragraph.<br />This is the third paragraph.</p>

Basically, I no longer have spaces between paragraphs, just line breaks.

In Wordpress 3.8.3, if I used the "paste as plain text" function, I got a little check box in the popup window that said "keep linebreaks." If I had this checked, I would get this:

<p>This is the first paragraph.</p>
<p>This is the second paragraph.</p>
<p>This is the third paragraph.</p>

... which is how I wanted it to show up.  But it looks like that option is gone in WP 3.9.

I don't want to have to go through every post hitting "backspace-return" at the beginning of every paragraph, and I don't want to have to mess with any kludgy workarounds ... I had to deal with those for years in systems like Zope, Saxotech, etc., and it was an incredible relief to find that none of that was necessary with Wordpress. 

Is there a way to modify CKEditor to make pasted returns show up as new paragraphs rather than just linebreaks?