She was evidently avoiding her husband and the relationship that must've thoroughly broken down by the time of the divorce proceeding and it is likely that she would be insecure about trusting him, not knowing whether he would be offended that Barack's Hawaiian citizenship was being used instead of his Kenyan citizenship. She simply could not rely on his silence.
Alternatively, she might not have secured the fraudulent Hawaiian birth certificate until after the divorce case because she was simply unaware of how easy the procedure might be and only learned from her attorney as another Freeper has suggested.
Of course it is also possible that Barack Obama was born in Hawaii and that the Kenyan certificate is a counterfeit. It is also possible that no birth certificate was needed or used in the Hawaii divorce case at all.