does "break some eggs"here a pun?
“That’s why I love you,” she said quietly. “Just that. It’s too early to call Tricia, and I don’t think either of us is going to get any more sleep. I’m going to make us some eggs.”
“That’s why I love you.” On a laugh, he turned to her, pulled her in. And as his gaze drifted over her head, he went still.
He saw, down at the point, a shimmer of light. “Wait.”
He moved quickly to the telescope, peered through. Straightening, he looked at Abra.
“He’s back.”
With a hand gripped on his arm, she looked for herself. “I kept wish-ing for this, so it could be done and over, but now that it is . . .” She took a moment to evaluate. “I feel the same way. Now, we do something.” She sent him a cool, fierce smile. “Let’s break some eggs.”
While she did so literally, and Eli made coffee, it struck him it might have been any morning, even if it started at barely five a.m.

Question

does "break some eggs"here a pun?
“That’s why I love you,” she said quietly. “Just that. It’s too early to call Tricia, and I don’t think either of us is going to get any more sleep. I’m going to make us some eggs.” 
“That’s why I love you.” On a laugh, he turned to her, pulled her in. And as his gaze drifted over her head, he went still. 
He saw, down at the point, a shimmer of light. “Wait.” 
He moved quickly to the telescope, peered through. Straightening, he looked at Abra. 
“He’s back.” 
With a hand gripped on his arm, she looked for herself. “I kept wish-ing for this, so it could be done and over, but now that it is . . .” She took a moment to evaluate. “I feel the same way. Now, we do something.” She sent him a cool, fierce smile. “Let’s break some eggs.” 
While she did so literally, and Eli made coffee, it struck him it might have been any morning, even if it started at barely five a.m.

Answer

"Let's break some eggs" means "Let us do some stuff even though we might get dirty, or it might be unpleasant."

It is a short form of another older idiom "You can't make an omelette without breaking eggs."

This means the same thing: in order to make an omelette (accomplish something) you have to break some eggs and make your hands messy.

See: http://idioms.thefreedictionary.com/You+can't+make+an+omelette+without+breaking+eggs

I would not call it pun, because there is no play on words. It is just an idiom, where the words are not meant to be taken literally.

An example of a pun would be if you said "Break an egg!" instead of "Break a leg!", say at a cooking contest. ("Break a leg" means "good luck" and can be used in any context; but if you said "Break an egg" instead of "Break a leg" to wish someone good luck at a cooking contest, that would be a pun. The normal "leg" is replaced by "egg" because the context is cooking.)