Pages: Make auto dash to break a word to new line (hyphenation-Greek)

You cannot disable these swashes using the Smart Swashes section in the Format » Font » Show Fonts » Typography… window, because they're not Word Final Swashes. Those are disabled by default anyway.

What you're seeing are Line Final Swashes, applied only to the end of a line or a text run with consistent formatting.

I found no option to disable them from the Typography window or any menu option.

What seems to work is to end a line by pressing Shift-Return instead of Return.

Note that this will not end the paragraph and allow you to apply a different paragraph style to the second line, so depending on your circumstances (e.g. use in Headings), this will not be an optimal solution.

You can, for example, make the next line font size 1 and only insert a single space character. In the following example, I entered a single A character of font size 1 to the next line so it's visible as a black dot:

It's an ugly hack, but it might work for you.

Pages is not at all set up to do what you ask. The layout in iBooks author is superior to Pages, but you can't easily share that work across platforms and until the next versions of Apple OS ship (presumably in the fall of 2013) - iBooks author lets you design on Mac only and read on iPad only.

The text in multiple columns flows from the bottom of one column and up into the next. Additions and deletions will not align well unless you use a table structure to hold paragraphs and enforce the right-left constraint so that one comment isn't higher or lower vertically than the text for which it corresponds.

Hopefully tables works for you, as your other option in Pages is to use the comments or track changes feature to anchor some amount of text to another specific portion of text. These items do print nicely, and you might find you can use the whole width of your page and let the software reduce things to fit as needed.