Mijn opinietje: I think alleen is more in the vein of "alone; sole"; alleen weet ik jouw geheim: only/just/solely I know your secret. Whereas one of the other meanings of 'maar' is 'but', and maar-as-alone here seems to be...not quite an intensifier, but kind of. "Is this but X?" is a bit of a poetic/archaic construction, but I've seen it: Are these laws but symbolic? (You're emphasizing the treatment of the laws as mere gestures and not binding dictates). Are we but two fools in love, pining for someting we could never have? (You're emphasizing that we might think otherwise, but we're no more than two fools.)
Or for tl/dr: I'm guessing alleen is akin to 'alone' and maar is akin to 'mere.'