Answer:
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"A friend in need is a friend indeed" is the correct quotation, though your version - "a friend in need is friend in deed" is more apt and far less ambiguous than the original, or at least than the version we're currently familiar with.
It isn't known who wrote the phrase, though Oxford states it may be traced it back to the eleventh century.
It is sometimes read to mean that a friend you can help (a friend in need) is, or becomes, a true friend to you (a friend indeed), but this isn't supported by examples the phrase is generally used to illustrate, or by a knowledge of human nature!
Making more sense is the popularly accepted interpretation, which is that a person who is your friend and who supports you when you are in need, is indeed a true friend.
This is why your use of "in deed" struck me as apt. Whether you've written it that way deliberately or by accident, your version clearly states that someone who supports you in your time of need is behaving in the way a true friend should (a friend in deed).
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it means that if your friend is a true friend then they will come to you for help