Can trade secret protection really be an alternative to patent protection for startups?

Perhaps you need to sit and down and figure out exactly what is the value that you wish to protect. Keep in mind that with software, any functionality can be duplicated (in time). Trade secrets is essentially based on the relationship and the legitimate means of accessing or deducing that secret, so whilst a non-compete can be enforced with employee, your competitor can reverse engineer your product with no recourse. Your secret could be preserved via keeping core software on a limited number of servers (PaaS), careful marking of documents with warnings (in confidence or privileged) and generally IT security practices. Courts need to be convinced that you adequately secured your "property" but keep in mind that "property" does not usually extend to vague business ideas as there may be multiple alternatives in a small space. So understand that "protection" is only with those you have a formal relationship with as evidenced by legal agreement, not to unrelated third parties and does not apply to information which is generally "known" (know-how v proprietary knowledge).