To answer the question with a quick how to:
Without going into details about how to write css for a book, you can 'fix' small things like this in Calibre by Converting the book... It's ok to do Epub to Epub conversion.. you should make sure you have a original copy of your book saved somewhere outside of calibre, in case you are not happy with the changes made here.
When you press the convert button on an book, in the left hand column, is a "Look and Feel" catagory.
I would suggest first putting a check mark in "Disable Font Scalling." Font scalling is a powerful and very useful tool, but it can make unnexpected changes to your book, and should probably not be used unless needed/wanted.
Here you have two choices. If you think your book spaces the lines too closely together, you can ajust the "Minumum Line Height Percentage".. default is 120%, If you find that too crowded for your taste, try increasing it. This will not restore your ability to adjust on the fly in calibre settings.
If you would rather remove all line height coded in the book, change that minimum line height to 0. Also, you have to to click on the "Filter Style Information" tab. In the text for for Other CSS, enter "line-height" (without the quotes.). That should remove any hard coded line height in the book, and allow the user specified prefernece to work without interference.
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