Effects like the supernatural ability holy lance can be used on mundane, non-masterwork weapons
When the rules describe a specific ability, that specific ability may override a general rule. So when a creature possessing the Good domain employs the supernatural ability holy lance, he really does "give a weapon [he] touch[es] the holy special weapon quality for a number of rounds equal to 1/2 [his] cleric level," ignoring the usual restriction that a weapon needs to possess at least a +1 magical enhancement bonus before the weapon can have weapon special abilities.
For much the same reason that, for example, a creature possessing the feat Power Attack specifically can deal extra damage despite the game having general rules for dealing damage, a creature that employs the supernatural ability holy lance really can touch any ol' weapon and grant that weapon the weapon special ability holy.
(An improvised weapon isn't usually crafted to be a weapon but is, instead, just another object used as a weapon, so that object's not, technically, a weapon, and that makes the object an invalid target for the supernatural ability holy lance—but since that sounds really close to gibberish to me, too, this GM would totally allow a level 8 cleric to bash somebody with a holy pool cue or frying pan or whatever, rules be damned.)
Anyway, special abilities often let a creature do things the rules say the creature normally can't. The game makes many general rules then breaks them with specific rules. So a weapon that's the subject of the supernatural ability holy lance gains the weapon special ability holy, masterwork or not, magical enhancement bonus or not, but such a weapon gains nothing else from the supernatural ability holy lance except what the lance ability says the weapon gains (e.g. no free +1 magical enhancement bonus).
(To confirm what is, essentially, my gut feeling, I did some research on this topic, and a similar question was asked about the inquistor's bane on the Paizo message boards in 2013, and that concern dismissed. Otherwise, the topic's unaddressed and seems to be played as described above.)
Note that a GM that nonetheless rules that the supernatural ability holy lance can only be used on weapons possessing at least a +1 magical enhancement bonus likewise limits a fairly large number of similar effects (the sorcerer bloodlines boreal's spell-like ability cold steel and stormborn's spell-like ability thunderstaff, the spell flames of the faithful, and the inquisitor's supernatural ability bane to name but a few). Were I playing a character with such an ability and such a ruling were made, such a ruling would be insufficient for me to leave the campaign, but I would appreciate it if the GM provided me the opportunity to make different choices for my character. Such effects will often be useless to characters level 5 and below, so under that ruling campaigns will end—and characters will die—before such effects can ever be used.