The literal meaning of wizardry is exactly that of your first definition: the name for the practice of wizards. Yet when applied in a metaphorical or illustrative way, the term 'wizardry', by itself, has no negative connotation. For that matter, as we're no longer given to the practice of setting fire to people, nor does 'sorcery'.
In fact both can be used to convey, quite neatly and playfully, a kind of baffled awe. For example, an article from The Economist remarked that 'MARIO DRAGHI seems more sorcerer than central banker', using the theme of magic and sorcery to illustrate the effect of his pronouncement of the Outright Monetary Transactions initiative, with such allusions as 'Who would bet against a central bank that can conjure money from thin air?' and 'Mr Draghi’s magic is powerful, but it won’t work without help from the politicians'. 'The ECB's bond-buying plan: casting a spell', The Economist.
In the article, the author describes how the yields on bonds issued by enfeebled Euro-zone economies tumbled after Mario Draghi, the head of the European Central Bank, literally stated that he would do 'whatever it takes' to save the Euro. Yet he didn't need to actually do anything beyond announce the fact: as if by magic, the panic of investors abated at the spell of his reassurances.
A Google search for your example of 'computer wizardry' reveals a number of companies who use the phrase 'wizardry' in either their names or tag-lines. I only checked the first page of results, but not one of those firms admitted to resorting to witchcraft and sacrifice in order to get great results.
A further anecdotal example would be when, late last year, some delivery men were able to fit my new and large sofa through a my old and small door, showing outright contempt for the laws of physics in doing so. I remarked that they were 'wizards' or 'magicians' (I don't remember 'witch' of the two (HA!)) and said I'd like to buy them each a pint. Rather than initiating slander charges, they accepted the tip I offered them in lieu of an actual beer and went merrily on their way.
'Wizardry' is a fun and descriptive word, and is a wonderful compliment to pay to somebody. If you were actually able to find somebody who took offence to its connections to witchcraft, I would advise you that this is a dangerous person and is not your friend.