First of all, while I haven't read the petition, I'm guessing that nobody is talking about making programming in certain languages a criminal offense (arguably unconstitutional and probably unenforceable); but rather that the petition is about prohibiting the use of certain programming languages by the federal government itself and in software the federal government uses. Since governments can and should make purchasing decisions in the same way any one else would, this should not offend anyone's libertarian sensibilities (if my wife and I don't want to use Windows in her yarn shop, that's our business, not anyone else's, to include MS').
Second, it should be noted that two of the most dangerous of all programming languages above the assembler level are also the most common: C (long notorious as a bug factory), and its superset, C++ (both are much more dangerous than Java ever thought of being) and that years ago, the US Defense Department spent large amounts of taxpayer money developing a specification for a best practices programming language that never really caught on in the private sector: Ada. So if the feds really wanted to promote safer computing, one of the things they could do is to make the language they've already paid to create easier to use, and to actively promote its use, at least in federal projects.
Third, it's an utter waste of time and effort to petition the President of the United States to do things he obviously does not have the legal authority to do. While this petition probably does not fall into this category, I've seen numerous others that do (like the various secession petitions) so the point should be kept in mind when filing new ones.