Does the Buddha's concept of Citta contradict the Mahayana doctrine of emptiness?

When you say Mahayana, I think maybe it's good to differentiate between Cittamatra and Madhyamaka, both Mahayana. For Cittamatra there's "mind only", and the mind is based in a mind basis of all mind. This mind basis of all in Cittamatra seems to be not empty of intrinsic nature, it seems to be the basis of all mind, existing in and of itself.

In Madhyamaka on the other hand there is no mind basis of all, there is only emptiness and the emptiness of emptiness. The Madhyamaka would perhaps say that Cittamatra has not negated enough, not taken into account the emptiness of emptiness.

This Wiki entry talks about the meaning of citta and the different ways various traditions have conceived of the purified, luminous citta. As is the case for all appearances (whether pure or impure) there is no contradiction between appearance and emptiness from a Mahayana perspective (at least the Indo-Tibetan flavor): citta is not taken as having true, inherent existence in the reified and impossible sense that is refuted by the view of emptiness. As simply one example of the coalescence of appearances and emptiness, go back to the Heart Sutra. In Thich Nhat Hanh's lovely translation:

this Body itself is Emptiness and Emptiness itself is this Body. This Body is not other than Emptiness and Emptiness is not other than this Body. The same is true of Feelings, Perceptions, Mental Formations, and Consciousness.

As one's understanding of emptiness and dependent origination deepens, the reasoning that "things appear because they are empty, and are empty because they appear" actually becomes quite compelling and seems quite simple (though profound) when compared to more elaborate analyses such as the "vajra splinters" reasoning (referenced here).

While citta seems to show some variations according to context, it's literal meaning is "thought", but also has been identified primarily with "state of mind". Here's Sue Hamilton analysis¹:

By this I mean that citta is the term used to refer to the qualitative picture, as it were, of the way all one's mental processes are functioning at any given moment. This is very different from any of the different mental processes of which the whole 'mind' is comprised: citta is neither an entity nor a process (which probably accounts for its not being classified as a khandha, nor mentioned in the paticcasamuppada formula), but is a term which abstractly indicates one's progress on the path, or even more generally, one's mental condition.

[...]

Understanding citta to mean 'state of mind' clarifies otherwise confusing passages, such as the following examples: "Without understanding the thoughts of his mind, one is reborn in life after life [...] with a restless state of mind". Likewise: "My state of mind is not of such nature that it will return to kamabhava levels of existence; knowing this, one's state of mind is well acquainted with wisdom". Johansson suggests these (and other similar) passages imply that citta "seems to signify a surviving entity". But what they are indicating is that one's state of mind reflects one's progress, or lack of it, on the path to insight.

Claiming that citta is everlasting is not just a challenge to suññatā, but a challenge to anatta, and thus, a contradiction to pretty much the entire canon on that matter (whose summary has been written as sabbe dhamma anatta: all dhammas are not-self). Finally:

"Bhikkhus, you may well cling to that doctrine of self that would not arouse sorrow, lamentation, pain, grief, and despair in one who clings to it. But do you see any such doctrine of self, bhikkhus?"
—"No, venerable sir."
—"Good, bhikkhus. I too do not see any doctrine of self that would not arouse sorrow, lamentation, pain, grief, and despair in one who clings to it."

-- MN 22

¹ See "Identity and Experience: The Constitution of the Human Being According to Early Buddhism"