tl;dr version: Marks are offered for a guild randomly selected from among those a) in which the player meets the recommended rank, and b) are located in the city-state the guildleve is being viewed in. Fulfilling the objectives of the levequest as a class other than this will yield fewer marks (down to a minimum of 0).
After some thorough fact-checking, I'd like to reply to this thread with an explanation of the mechanics at work behind this system message.
By way of an example, let us assume we have a character with the following classes: thaumaturge (rank 30, Ul'dahn guild), conjurer (rank 35, Gridanian guild), and archer (rank 33, Gridanian guild), and lancer (rank 17, Gridanian guild). On a battlecraft guildleve, the guild for which marks are offered as a reward is selected at random from among those guilds a) in which the player meets the guildleve's recommended rank, and b) which are located in the city-state where the guildleve is being viewed.
Therefore, in the case of the above character, a rank 30 guildleve in Gridania would offer guild marks for either conjurer or archer. Thaumaturge marks would not be offered, since that guild is located in Ul'dah, and neither would lancer marks, as the character's rank in that class is not high enough. To be clear, both the regional and rank conditions must be met.
The class which appears in the system message in question (below) is the one that is randomly selected in the manner described above.
Completing this levequest as a class other than [[class]] will reward fewer guild marks.
What this message attempts to convey is that fulfilling the objectives as a class
other than that for which guild marks are being offered will yield fewer marks. As AdvancedWind stated, killing half of the target enemies as the appropriate class and half as another class will yield half the guild marks. In the most extreme case, as Anonymoose experienced, killing all of the target enemies as another class will yield 0 marks. I understand that "fewer" may be misleading in regards to the latter, but we wrote the message this way to keep it simple while still accounting for both zero and non-zero values.
It is also worth noting that only the actual fulfilling of the objectives as another class will lessen the amount of guild marks awarded. For example, if the guildleve calls for the extermination of 10 monsters, only the slaying of those monsters as another class lessens the amount of guild marks you receive. Other elements such as the class you are while traveling to the levequest location, or the class you are at the time you turn the levequest in, etc. will have no effect.
I
hope that clears things up...