The term "conspiracy theory" exists in its own right in the English language (quite separately from "theory" at this point) and is not a scientific term in any way, shape or form. It does not rely on the scientific meaning of "theory", but rather the colloquial one. Your omission of that fact makes your question somewhat misleading. After all, it doesn't make you "wrong" to correctly identify a butterfly, even if it's not a flying piece of butter, or a fly made of butter, or even an insect that's buttery in colour.
This may be of help:
http://dictionary.cambridge.org/dictionary/british/conspiracy-theoryhttp://dictionary.cambridge.org/dictionary/american-english/theory (note that the scientific use is distinguished, but not the sole accepted use)
http://www.oxforddictionaries.com/definition/english/theory (as above, but also see 1.2)
It is very important to keep in mind that language serves a certain purpose, and that is to facilitate efficient communication. Some words gain very specific meanings (for example "rape", which originally meant "to seize by force" but also "to hasten", is unlikely to be used to mean anything other than forced sexual intercourse), while others become somewhat more general (for example the noun "lock", which used to refer only to a mechanism or enclosure, but has since been extended to include more abstract things like mutexes). Some words may have different meanings depending on which context they're used in ("theory" is a great example here. In theory, it should be clear what is meant by "conspiracy theory", but in practice you chose to misunderstand it).
In other words, no, we're not misusing a scientific term. We're not trying to use a scientific term to begin with, because "conspiracy theory" is not one. Importantly, however, it's a term that's been
acknowledged by researchers worldwide, and a term whose meaning is generally not seen as ambiguous, as long as the context in which the words were used is known.