I'm not sure I understand the problem description. Turning on prettification does breaks table alignment; thus,
| a | b | c |
|--------+---+---|
| \alpha | | |
is always displayed as
| a | b | c |
|--------+---+---|
| α | | |
I can indeed reproduce this; one way to prevent it from happening would be to prettify "\alpha" as "α “.
This is the same as my experience, and it makes sense because turning on prettification does not take care of the alignment. The problem I have is exactly related to what you described below, i.e. the table alignment after a realignment.
On the other hand, realigning the table (by pressing tab in a cell) produces the expected alignment:
| a | b | c |
|---+---+---|
| α | | |
I have a different experience for this.
In my case, after a realignment (by pressing TAB or C-c C-c), I got
| a | b | c |
|----+---+---|
| α | | |
instead of
| a | b | c |
|---+---+---|
| α | | |
It looks like that a greek letter is considered to be a double-wide symbol but displayed as a single-wide one.
which in turn looks wrong when prettification is disabled:
| a | b | c |
|---+---+---|
| \alpha | | |
Does this match your experience? If so, I don't think it's a bug, as much as a limitation of prettification.
Clément.
This is surprising as I can reproduce the issue with a clean init file.
Btw, I am using org-plus-contrib package (20160822) with emacs 25.1.50 on a mac (10.11.6).