It's a good question, and one I suspect you're unlikely to get a straight answer to because the evidence isn't clear at that altitude. Certainly at considerably higher levels (>4000m) there are a whole raft of problems that occur more frequently - delayed growth and more jaundice in the newborn, and high blood pressure for the mother - but at lower levels I can't find much useful data. Most people would agree that at these altitudes whilst the pregnancy may be entirely unaffected the risk of problems - and also the difficulty in reaching medical attention if they occur - is considerably greater.
As Alex says, Alison Hargreaves climbed the Eigerwand whilst about 18 weeks pregnant but according to her biographers had significant misgivings about doing so after the event - and certainly got a lot of flak for choosing to do so, mostly from uninformed media commentators.
At 3000m, the air pressure will have dropped from about 760mmhg at sea level to 560mmhg - ie about 25% - and oxygen pressure in the lungs will have dropped by about 40%. The air pressure in the plane on the way to your holiday is kept equivalent to 1800m (or up to 2400m in the real skinflint airlines like Quantas). Pilots aren't allowed to fly at higher than this equivalent cabin pressure without using additional oxygen, but then they don't have the advantage of slow acclimatisation.
The fetal circulation is designed to cope with lower oxygen pressures - using a different type of haemoglobin - and so has a degree of protection from lower oxygen levels that could occur during labour, but even so it will be starting from a lower level, and it isn't clear what the effects of this could be on development. As Jon says, the risk is probably greater at the early and late stages of pregnancy rather than the more stable growth phase in the middle. I suppose the question that you have to ask is if - heaven forbid - the baby is born with problems that could have been caused by lack of oxygen during development, would you blame yourself?
Overall I would suggest sensible precautions like slow ascent and a relatively low maximum altitude - by which I mean 2500 - 3000m max - would be safest, but it's your choice.
I'll try and find out if the Expedition Medicine centre is still going at Barts (Dr Charles Clarke, an old friend of Sir Christian B usedd to run it). Otherwise you could also contact the Royal Geographical Society Expedition Advisory Centre.
Goood luck!