Yes, we do consider it a language.
While the exact definition of what is a language is debated, in Bavaria we do refer to it as a separate language with its own poetry, literature and grammar rules. Its difference from regular German is so extreme, most non-Bavarians can not understand most of what is said and Bavarian language interviews or programs need to be subtitled in German. According to UNESCO it is an endangered and protected language. Also, within Bavaria itself, Bavarian has its own dialects and variations, primarily separated into north, middle and south Bavarian.
North, Middle and South Bavarian within Europe
As for origin, it developed alongside and separated from German and the many other dialects in the region. Like German and English it is of Indo Germanic origins and containing a lot of Latin elements. As such it contributed to the development of modern German.
Think of it as Bavarian being to German, what Scottish is to English.