No, potions of healing don't hurt undead (unless you hit them really really hard with the vial).
Monsters and NPC usually have 1 healing surge per tier, and potions are one of the few ways they are able to tap on them. Some humanoid monsters from early monster manuals have the Second Wind power explicitly listed in their stat block (most template-created intelligent undead, for example).
The following healing potions (those that appear on the Player's Handbook) require the user to spend a healing surge in order to gain their effect.
The following potions, however, function even if the imbiber is bloodied and has no healing surges left. They can be found in the Mordenkainen's Magnificent Emporium.
Positive and negative energy is a thing of previous edition. In 4th edition, radiant and necrotic are damage type keywords, but they are not intrinsically tied to the healing keyword or mechanics.
For example, some undead have healing powers (like the Skull Lord, the Spirit Devourer, or the Voidsoul Specter).
The way you handled the thing was, in my opinion, correct. You gave the hint to your players that the healing keyword does not mean radiant damage.
Edit: In a previous version of this answer I stated that monsters usually have no healing surge. This is false, as @wax eagle pointed out.