Methods are provided for improved quenching of undesired side reactions upon treating a red blood cell composition with a pathogen inactivating compound comprising a nucleic acid binding ligand and a functional group which is, or which is capable of forming, an electrophilic group. In some embodiments, the improved methods use a suitably high concentration of quencher that comprises a nucleophilic functional group that is capable of covalently reacting with the electrophilic group, wherein the treatment occurs within a desired pH range to provide sufficient quenching. Preferred quenchers for use in some of the methods include thiols, such as glutathione, which have been suitably neutralized such that addition to a red blood cell composition results in the desired concentration of quencher at a desirable pH range of 6.8 to 8.5.