If the SAP system is correctly configured, pulling data is not impacting its performance.
SAP ERP has the possibility to make parallel jobs, with appropriate ressources.
Otherwise, doing a request in SAP through SE16N would also impact the system...
A SAP Basis should help you to measure that.
Loading a big amount of data can have an impact on the network.
In this case, try to locate the QlikView Server on an appropriate place (if SAP is hosted, can QlikView be hosted in the same datacenter ? Avoid VPN connexions, and so on)...
To limit the amount of data, you should work on delta load, when it is possible...
Unfortunately, I do not know a global solution that would always work... it is related to tables.
Tip : you can look how BW and other BI tools take data from SAP to find the appropriate method.
Moreover, the SUBSELECT option from Qlik Connector can be very usefull.
Hope it helps...