The person responsible for buying suppies for our office says that she doesn’t buy from a shop which is owned by Jews and which opens on Shabbat. Is there any halachic basis, either for Ashkenazim or Sefardim, for not buying non-cooked items off the shelf (milk, tea, coffee etc) from a convenience store owned by Jews and which trades on Shabbat and where no cooking takes place?

There is a rabbinical prohibition of "mesaye'a l'ovrei aveira" = which means assisting a transgressor in carrying out his sin. (See Tosafot Shabbat 3a, Rosh Shabbat 1:1, Rema yoreh De'ah 151:1, Tziz Eliezer 20:20)) However, this does not apply here since by buying coffee there is no direct assistance in desecrating Shabbat. Some people though, out of sentiment or protest prefer not to support those who desecrate Shabbat. May we find ways of pleasantness and peace to bring our brethren closer to keeping Shabbat.