Yes, slang, profanity, and this sort of muted or pseudo-profanity don't necessarily follow the conventional rules of grammar.
When these sort of words are used as adjectives, they are at least grammatically consistent. If we assume that "to freak" is a verb that presumably means something bad or unpleasant, then, "Make your freaking dog stop barking" makes some sense: the speaker want to express that the dog is doing something unpleasant, so if "to freak" is bad, then describing the dog as a "freaking dog" means he is doing something bad. Of course when taken more literally, it still doesn't make much sense. I presume when people say "to freak" they are using that as a euphemism for another word that begins and ends with the same letters and that refers to sexual activity, and the dog in question is probably not engaging in sex. The train but surely is not.
As an adverb -- "Just freaking go", it makes no grammatical sense. You could say, "Just go freakingly", but what does that actually mean? Sometimes people say, "Go freak yourself", which again is unlikely to resolve the immediate issue or be physically possible, but at least is grammatically coherent.
Of course we don't normally expect insults and profanity to make literal sense. They're just words added to a sentence to express anger or dislike, or to establish yourself as one of the cool people who use such words. The f-word, in particular, rarely makes sense in context if interpreted literally.
Most slang words, whether mild or vulgar, are not being used for their literal meaning, but rather are used to mean either "bad" or "good". There are probably dozens or hundreds of slang words in use at any given time that all mean "bad" or "good", from "groovy" to "cool" to "phat", etc.