Assuming you are talking about a normal campaign using Standard Priority character generation methods, there are a few caveats to being allowed to start with an Ally. First, is the fact that it is commonly disputed whether Initiation is allowable during character creation. On the one hand, it isn't on the chart during the character creation chapter, but on the other hand it is never stated that the chart there is everything you are allowed to do. So, that right there, means it is GM permission just to initiate at chargen. This costs 13 karma
Second, creating an ally spirit is normally a prolonged process requiring several things to be able to accomplish. You must have the spirits formula, which either requires an astral quest (which non-initiates cannot do), or decent training in Arcana to be able to write one yourself (or extreme trust in someone else to do it). It also requires you to successfully summon and bind the spirit normally (see FancyDerek's post about what happens if you try to create to large of an Ally, or try to summon/bind too large a spirit in general). This whole process is also not usually considered to be "handwave-able" it is difficult and a character should work for it. So it is also pretty high up on the list of things you should be wary as a GM just "allowing" him to do. An Ally costs a minimum of 8*Force in karma to create.
Lastly is those karma costs. Under normal creation rules, utilizing the Priority method, the absolute maximum karma a character can have is 50 (25 to start + 25 from negative qualities). The maximum Force you could possibly create at chargen, assuming a GM allows you to do so would a Force 4, which would cost 32 karma base plus the 13 for the initiation. This would leave you with 5 karma to round out the character, maybe get one of the smaller positive qualities. Not much, considering you had to take the full allotment of negatives for this.
Personally, I wouldn't necessarily wave it away out of hand, but I would only allow such a thing if the character being made had some great story behind it about why an only moderately experienced Shadowrunner Magician would have that circumstance right out of the box. From the sound of things, based on the way you asked the question, I don't think your player has something amazing in mind. It seems like they are just trying to game the system and get a leg up on things by taking advantage of those spirit mechanics. Immediate territory for GM veto.
