No.
There's a certain snobbery about people who had their act together. Not everyone knew what they wanted to do as an undergrad. You might have more aptitude than people with a BS CS. Pick a program that doesn't treat you as a cash-cow: one where you can take the same courses as undergraduates and PhD students. Then ignore nay-sayers.
If it's a two-year program, you can likely get enough courses in to learn something serious. I have less respect for one-year BS/MS masters programs simply because you won't be taking that much. In two years, you could take 12-16 courses and maybe do some research in the second year.
When it comes to university credentials, people like to "lock-in" their value. If you went to Harvard, no matter how much of a failure you turn out to be, you went to Harvard and people should respect you. So, if I have a BSCS, there's a great temptation to say, "no, you can't go back in time and get to the same level as me. Even if I'm incompetent at my job, employers should devalue you no matter how good you are because you're that 'absolute lowest form of life in software engineering'". But we shouldn't think that way. You're trying to better yourself. Kudos!
To be realistic, you might come out of the program not on-par with the type of student that would be capable of applying to top PhD programs, depending on how rigorous your courses are. Two years can be a short time, especially if you're starting with intro to programming. However, if it's a good program, I think you can come out well among those looking for software engineering jobs.