The biotin-streptavidin interaction is extremely strong, one of the strongest (if not the strongest) non-covalent interaction between biomolecules. So you'll need pretty harsh conditions in any case.
Extreme pH values are generally a very bad idea for RNA. I'm pretty sure that the conditions you mentioned are not meant for elution of nucleic acids. Such low pH values (and high pH values as well) lead to a quick hydrolysis of the phosphoester bond of RNA, you can read more about the mechanism of that in this review.
A quick Google search lead me to the following protocol:
To dissociate biotinylated nucleic acids from Streptavidin-Coupled
Dynabeads®, incubate the beads in 95% formamide + 10mM EDTA, pH 8.2
for 5 minutes at 65°C or for 2 minutes at 90°C.
This sounds reasonable to me, as formamide is also commonly used in sample buffer for denaturing gel electrophoresis of RNA. I haven't done anything like that myself, so I can't guarantee that this would work in your case.